Gene Warfare
by Rowana Farrin
Summary: Carson and Ronon are capture by Wraith with an eye for Ancient technology, but an impending invasion interferes team's attempts to rescue them and puts the whole of Atlantis in jeopardy as their own weapons are turned against them. No pairings. FINISHED
1. Chapter 1

**Disclaimer**: Sadly, I do not own any of these characters. I only take them out to play.

**Timeline/Spoilers**: Takes place in Season Two, sometime after "The Hive" and before "Micheal." Contains spoilers for "Instinct" and "Conversion" and minor spoilers for other episodes.

**Author's Note**: This is my first post in a long time, though I actually started this story last year. The original idea was conceived for Ree'an, my original character, but I have changed it around and like it better without her. It does contain Jamie from my other stories: "Dragons of the Deep" and "Dolittle Device."

Many thanks to NalanaSpinderOfSouls and my other friends for beta reading! Hope you people enjoy it and please review and tell me what you think! Reviews make me happy and happy writers write better stories!

Gene Warfare

By Rowana Farrin

**Chapter One**

_Silence. It penetrated every hallway of the dark city. Not a sound echoed in the unending corridors. Nothing moved. Even the shadows did not so much as quiver. All was quiet, wrapped in a blanket of disturbing silence. Darkness too haunted the halls. Thick and intangible, it hung like a cloud over the city. Lights that dared shine were immediately swallowed by the unforgiving dark._

_Amidst the darkness and silence, an evil lurked. Its presence was clear against the tranquility of the city and the sea that surrounded it. The evil stalked the corridors, searching. Searching for something that it needed to find. Something that it needed to spread its menace throughout the worlds. It was hungry. It was thirsting for the lifeblood of innocents and their screams of terror as they died._

Teyla woke with a start, the memory of the nightmare still fresh in her mind. Something was horribly wrong. Something was here; something that should never have been here. She threw off her covers and raced down the halls. Her running feet and panting breath broke the blanket of silence. The city was suddenly alive again with the noise that normally plagued it. She pelted around corners and down dark passageways until she finally reached her goal. She knocked frantically on the door, as the cold dread in her mind grew.

"Colonel Sheppard! Wake up now!"

John woke with a start. It figured that the one night he seemed to be having a peaceful sleep, someone would knock on his door. He groaned, rolled over, and rose quickly to deal with whatever emergency had come up this time. He grabbed his gun and opened the door to find a barely dressed Teyla. Before he could ask what was wrong, she answered the question: "Wraith. In the city."

He frowned and instantly reached for his gear. "Are you sure about that?"

"Yes. I do not know how, but they are here." She froze suddenly. "Wait..."

"What is it?" He glanced around the corridor, gun ready to shoot anything that threatened.

"I believe they have gone. But they were here!" she insisted.

"Right." He made a quick discussion. "Go and wake Dr. Weir, tell her what's going on and to meet me in command." He grabbed an extra gun and radio from his room and handed them to her. "Be careful."

Teyla nodded and headed off. John ran for command, checking each corridor as he went. All was quiet and looked normal. He knocked urgently on his new second in command's door.

"Wraith in the city," he told a startled Major Lorne when he opened the door. "Have security teams sweep every inch of the city. Check in every ten minutes."

"Yes, sir." Lorne immediately began to radio his men while he pulled on his combat vest. Sheppard didn't wait, but hurried quickly on towards the command center.

Teyla and Dr. Weir were already waiting for him when he got there. Dr. McKay had also been awake, doing late night lab, work and was now typing frantically on one of the laptops. Sheppard immediately started pumping the night crew with questions: "What's our status?"

The tech on duty shook his head in confusion. "Scans are clear, sir."

"Are any of the systems affected," Dr. Weir asked.

McKay barely looked up. "It's going to take a while to run full diagnostics. But there are hundreds of systems to go through and we have no idea what the Wraith could have done to affect them." He sounded nervous, but so far was keeping himself under control. "What worries me more is how they got in without anyone knowing. The scans should have warned us of if any showed up."

Sheppard frowned and started pacing the floor. His instincts were screaming that something was wrong, but he couldn't put his finger on it. He clicked his radio. "Lorne, report."

"No sign of the Wraith, sir," the Major replied. "Everything seems quiet."

"Start checking the crew quarters. I want a full head count on all personnel and let me know the minute anyone is missing."

"Yes, sir."

Impatient for results, Sheppard and Teyla took off and met up with Lorne and Lt. Cadman in the South hall. Sheppard and Major Lorne started down the living quarters taking a count of each person. Teyla and Cadman did the same in the women's quarters. Most of the other personnel were asleep and the rest were more than willing to stay in bed until danger had passed.

After several minutes without incident, John was beginning to think they had gotten away clean this time. McKay reported that the computer and technical systems were untouched and so far all the patrols had come up negative. It bothered John that the Wraith didn't seem to have done anything. Sneaking around wasn't like them in the first place and to leave without hurting anyone or anything was definitely out of character. Still, he had a few more corridors to search.

He turned a corner and immediately knew something was wrong. The hall looked the same as all the others, but something was definitely not right. Major Lorne started checking doors. Everyone was asleep and most didn't even notice the soldier checking on them. Sheppard walked ahead uneasily, weapon armed and ready. Suddenly his foot hit something that skidded loudly across the floor. Lorne looked over, gun ready, but Sheppard held up his hand in a silent command to wait. He knelt and picked up the object. It was a hunting knife with a wood and leather hilt.

'_This is Ronon's knife,' _he thought in puzzlement_. 'What would he be doing here in the middle of the night?'_ He felt a sinking feeling in his gut. The knife was covered in fresh red blood.

"What is it?" Lorne asked softly.

"I don't know." He turned quickly to the door that the knife had been by and quickly palmed it open. In an instant his worst fears were realized. The room was in shambles. Sheets had been torn off the bed and thrown carelessly aside. The side table had been knocked over and personal affects were strewn all over the small room.

John looked at the scene in horror and barely heard Lorne's next question: "Whose room is this?"

He felt his heart sink even more as the answer came to him: "Dr. Beckett's."

To be continued….


	2. Chapter 2

Gene Warfare, by Rowana Farrin

**Chapter Two**

"Colonel!" A soldier's voice broke John from his stupor.

He reached for his radio. "Go ahead."

"Ronon Dex is not in his room, sir," came the concerned report.

"Understood," Sheppard replied. He glanced down at the knife in his hand. "Everyone, report to the south west hall. I've found something." He spoke on autopilot, barely comprehending his own words.

"What is it?" Weir asked.

John couldn't bring himself to say it. "You'd better see for yourself."

In a matter of moments, Teyla, Weir, McKay, Cadman and several more security personal had gathered in the hallway. Curious heads also poked out from nearby doors. Sheppard still stood in front of the doorway, but was recovering from his shock quickly.

"Well?" Weir asked. "What have you found?"

John decided to get straight to the point. "Ronon and Dr. Beckett are missing."

The others were taken aback.

"Are you sure they aren't just somewhere else in the city?" McKay asked hopefully. "Carson hardly ever sleeps, you know."

"I'm pretty sure." He stepped sideways to reveal the chaos of the physician's room. McKay's mouth fell open in horror and Cadman eyes widened in shock.

"Oh my God," Elizabeth gasped.

"I found this outside," Sheppard added, showing them the knife.

Dr. Weir took a deep breath to calm herself and immediately started assessing the situation. "Teyla, are you sure the Wraith have gone?"

"Yes. I have not felt their presence for some time."

Weir nodded in understanding. "Major Lorne, is anyone else missing?"

"No, ma'am. All other personnel are accounted for."

She frowned. "So, this was all they came for?"

"What would they want with him?" McKay asked in frustration. He was desperately trying to grasp anything that would help him accept what was happening. It wasn't easy. Of all the people who might have been captured, Carson seemed to be the least probable. He was a doctor, after all not a soldier, and the Wraith certainly had no need for medical knowledge. At least, so they thought.

"I don't know," Sheppard replied, keeping his voice level. "But he was certainly what they came for. They didn't touch anything else. Not even the generators. Ronon must have caught them and was knocked out before he could radio for help." He didn't add that Ronon could have been killed. He wasn't going to go there, yet.

"But what use could he possibly be to them," Weir asked in frustration. "If they just wanted a prisoner, they could have taken anyone. And why take only him? Why not steal some of the Ancient technology? That would probably be more valuable to them."

John stared at her as a sudden thought occurred to him. "That's it!"

"What's it?" McKay asked eagerly.

"The Ancient technology!"

"You're not making any sense," McKay sighed impatiently.

"What's the biggest contribution that Beckett's made to this program?"

"Well, his research on the ATA gene and the retrovirus has been invaluable," Weir stated.

Sheppard snapped his fingers. "Exactly!"

McKay stared at him, aghast. "The gene therapy," he said softly. "If they get that, there'll be no stopping them!"

"Relax," Weir told him. "Carson isn't fool enough to just hand it over."

"And if he doesn't?" McKay trailed off. He didn't have to finish. They all knew what happened to people the Wraith no longer had a use for. "We have got to find him! Now!" he snapped with renewed determination.

"That's not going to be easy," Weir told him unhappily. "As yet, we still don't know how they got here and away without us knowing about it."

"And standing here talking is just wasting time!" McKay barked emphatically.

"Fine," Weir gave in. "Take Zelenka and anyone else you need and find out how they got in and how to track them. Sheppard, you and your team need to find out where the Wraith got into the city and see if you can figure out anything useful from that." Sheppard seemed about to protest, but Elizabeth cut him off. "This is all we can do right now. Hopefully, we'll find something that will lead us in the right direction."

Everyone took off in various directions, eager to get started. Even though it was the middle of the night, no one would get any sleep until their friends were back safe in Atlantis. Sheppard and his team headed down the hall to look for the Wraith's point of entry while Dr. Weir went back to command to contact Colonel Caldwell on the Daedalus. As much as she wanted to keep this under her jurisdiction, they might need the vessel to mount a rescue mission. McKay went to wake Dr. Zelenka. He was impatient to get started and banged loudly on the Czech's door. He needn't have bothered. The smaller man was already waiting to hear what had been the cause of the alarm. He was surprised, but not unprepared, to see a breathless Rodney at his door. He opened his mouth to ask, but McKay beat him to it. "Research lab. Now. We've got work to do." Without waiting for an answer, he turned and started off.

Zelenka ran to catch up. "What is going on? Why the hurry?"

McKay didn't even slow down. "Beckett and Ronon have been taken by the Wraith. We have to find out where they went; sooner rather than later."

Radek was still a little confused, but he understood the urgency of the situation. He quickened his pace. They really did have work to do and the faster they got started the better. "I'll check the deep space sensors," he said.

"They would have shown up sooner than this!" McKay said in exasperation. He was frustrated and in no mood to waste time on useless efforts.

"Or there could be something wrong with the circuitry," Zelenka explained calmly. "We'll never know until we check."

McKay sighed. "Alright, alright. Let me know the moment you have anything. I'll be in the main lab."

Zelenka nodded and ran for the control tower. Dr. Weir was already there, updating Colonel Caldwell on their situation. Zelenka went straight for the tech on duty. "Has anyone checked deep space sensors?" he asked breathlessly.

"No," the baffled tech replied. "Why?"

Zelenka let off a stream of curses in his native language before pushing the man aside impatiently. He typed madly on the keys, not even glancing up as Weir moved to look over his shoulder. He frowned. The screen was blank, as he had expected, but something was off. He fiddled with the settings, trying to fine-tune the sensors. Then, it appeared: a tiny dot, just behind the planet.

"What is that?" Weir asked.

"A hyperspace anomaly. A small one."

"Wraith?" she asked urgently.

"According to the scanners, it is Ancient, but I am not so sure. The readings are abnormal." Zelenka paused to push his glasses back in place. "It is possible that the Wraith are using an Ancient energy signature to hide their approach."

"Can they do that?"

"I can not be sure, but it is the only way they could have approached without the sensors giving a warning."

"How big is it?"

"Small. Larger than a dart, but not as big as a cruiser."

"Alright. Find out where they're going and report back to me," she clicked her radio. "Colonel Sheppard?"

"Sheppard, here," came the reply.

"Dr. Zelenka thinks he's found how the Wraith were able to approach the city. Found anything on your end?"

"We found the doors to one of the balconies open. They must have been scooped up by a ship. Did Zelenka find out where they went?"

"He's working on it. In the meantime, why don't you check on McKay and see if he's found anything."

"Will do. Sheppard out," Sheppard turned of his radio and gestured to his team. "Head back to command and get ready to mount a rescue," he ordered. "Teyla and I will go see if the good doctor has any answers for us."

They found the scientist in his lab, typing frantically on one of the many laptops strewn around the crowded space. Sheppard came up behind him. "Find anything?"

McKay jumped, then gave a relieved sigh when he saw it was only his friends. "I wish you wouldn't do that," he said irritably, turning back to his work.

"Sorry," Sheppard said tersely. "So, have you found anything?"

Without looking up, McKay answered: "I've been going over what we know of Wraith hyperspace technology and based on the data Zelenka's been able to find, I think I may be able to determine where they are."

"That's good!" Sheppard was thrilled to finally hear some good news. "Let's go."

"It's not that simple," McKay said in frustration.

"Well then, make it 'that simple,'" Sheppard snapped. "We don't have a lot of time!"

"I'm working on it!" McKay snapped back.

"Enough!" Teyla interrupted. "This is not helping us find our friends."

The two men paused in their argument. Sheppard took a deep breath to get his temper under control. McKay mumbled an apology and turned back to his computer. The lab was quiet for several minutes except for the incessant taping of the keys. Suddenly McKay stood up and practically ran to other side of the room.

"What is it?" Sheppard asked eagerly.

"I think I have something," he tapped his radio. "Elizabeth."

The radio crackled into life. "I hope you have good news, Rodney."

"Thanks to the sensor data provided by Zelenka, I've been able to determine the direction that the Wraith ship was going when it left this system. Now, we know that Wraith hyper drive technology isn't that great, so if I'm right, they should make a stop near M3X209 within the next hour."

"That doesn't give us a lot of time," Weir pointed out. "Sheppard."

"I'm on it." Sheppard was already heading out the door with Teyla and McKay on his heels. "Lorne!" he called into his radio. "I want two teams of marines and three jumpers ready for an off-world rescue mission in five minutes!"

"Yes, sir!" Lorne called back happily.

By the time the three had reached the puddle jumper bay, Lorne, Cadman and a dozen heavily armed marines were ready and waiting for them. Sheppard nodded to his second-in-command before following McKay and Teyla into the last jumper.

As the ship descended into the gate room, Colonel Caldwell's voice came in on the radio: "Sheppard."

"Colonel," he replied tensely. He tried not to let his dislike for the man reach his voice.

"We can't afford to let that ship get through. Use any force to bring it down."

"I'll use any force I think is necessary to rescue our people!" he replied angrily.

"You can't let your personal feelings interfere with this," Caldwell insisted. "If the Wraith get their hands on Ancient technology, we could lose this war."

"I know," Sheppard said shortly.

"Be safe," Elizabeth called. "And bring them back."

"I will," he said firmly as the jumper disappeared through the Stargate.

TBC…

AN: Many thanks to all the wonderful people who reviewed! I've never gotten such a turn out for a story before and it makes me very happy! Next chapter will be more exciting and you'll see Carson and Ronon at last. I'm very busy this weekend so don't expect an update until late next week. Thank you again!


	3. Chapter 3

AN: I'm so sorry for the long delay. Please enjoy!

Gene Warfare, by Rowana Farrin

**Chapter Three**

The planet was rocky and deserted. Only a few scattered plants betrayed that it was even capable of supporting life. John didn't care. He cloaked the jumper and rose into space, closely followed by the other two jumpers. They fanned out in a wide pattern to cover as much space as possible and be in position when the Wraith arrived. Then, they waited.

"McKay," Sheppard said after nearly an hour, "where are they?"

"I don't know," he turned to look at his computer. "They should be here." .

"Perhaps they went to another planet?" Teyla suggested, though her heart sincerely wished it wasn't true.

"I hope not," said Sheppard, agreeing with the unspoken sentiment. "We won't get another shot at this."

"Wait," McKay interrupted. "Something's coming."

"Finally!" Sheppard hit the radio. "We've got incoming, prepare to engage!" He turned back to McKay. "What kind of ship are we dealing with?"

McKay barely heard the question. "I've never seen anything like this," he said, half to himself.

"McKay." Sheppard swiveled around. "When you say things like that, I get a little concerned."

"I'm sure it's nothing to worry about," McKay assured him.

"Alright," Sheppard replied with more confidence than he felt. Anything that bothered McKay could not be good news, but he wasn't going to let that stop him from rescuing his people.

Further discussion was cut off by the arrival of the ship in question. Larger than a dart, but not quite as big as a cruiser, it had an odd, bulky shape that seemed awkward, even in space. It popped into normal space just above Sheppard's jumper and neatly between the other two; a perfect position for an ambush.

"Lorne, Parker!" Sheppard barked at the other pilots. "Go for the hyperdrive and sub-light engines. Try to force them to land on the planet. Do not destroy the target!"

"I don't think that..." McKay began, but was cut off by the rapid fire of several drones from the other two jumpers. The drones seemed to be heading right on target before the glowing yellow shots went dark and stopped in mid-attack.

"What the...!" came the chorus of curses from Lorne and the other pilot.

"McKay!" Sheppard whirled around to look at him. He was sure the scientist knew something about this.

"I tried to warn you," McKay said indignantly. "The ship is emitting a signal just like one of the puddle jumpers. That's why it wasn't setting off the alarms at Atlantis. A similar signal prevents the drones from attacking it. It's a kind of fail-safe to avoid friendly fire."

"Well, turn it off!" Sheppard shouted angrily. They didn't have time for a science lecture. The ship could return to hyperspace at any moment.

"I'm working on it!" McKay snapped back. Even more so than the others, he was aware of the consequences if he could not. But cutting off the subtle signals that Ancient puddle jumpers used to communicate was like trying to stop freshman from talking in a lecture hall.

His efforts were hampered by the sudden jolt of the jumper as it was struck from behind. "Hey! I'm working here!" he shouted to the front.

"Sorry!" Sheppard shouted back in a tone that made it clear he wasn't. "Tell that to the Wraith shooting at us!"

The jumper veered, barely avoiding the blue bolts as the Wraith ship closed in on it. Lorne and Parker came in from behind and fired several more drones, which had as little effect as the first ones. The Wraith ship took no notice and continued to dog its target.

"Hang on!" Sheppard called to his passengers. He dove toward the planet and built up speed. The Wraith ship pursued until the jumper hid in the atmosphere. Then, it appeared to change its mind and shot back up towards Lorne's and Parker's jumpers.

Teyla glanced over at Sheppard in concern. "We do not appear to be slowing down."

John didn't answer her. He was too busy concentrating on keeping the jumper on course. His knuckles whitened from his grip on the shaking controls as he slowly pulled out of the dive. The jumper continued to fall closer and closer to the harsh landscape below them.

"Colonel!" McKay shouted in alarm. His eyes bugged at the rapidly approaching ground.

Sheppard leaned back and the jumper banked upward, just brushing the planet's surface. It careened onward back into the blackness of space. Sheppard frowned. Where was the Wraith ship? He clicked his radio. "Lorne! Parker!"

"Sorry, sir," came Lorne's reply. "We lost the target."

John's heart sank. He turned back to McKay. "Can you track them again?"

"No." The finality in his voice was worse than any sharp insult. "I might be able to extrapolate their destination based on data from the jumpers, but that will take hours." He didn't have to add that, by then, the Wraith would have moved on to another location.

"Then, we have lost them," Teyla said mournfully.

John clenched his teeth. He wasn't going to go there. He tapped the radio again. "Lorne. Parker. Let's go home." _Elizabeth's not going to like this_, he thought.

--------------------

Carson groaned. He felt sick and woozy. His whole body ached and tingled. That couldn't be good. He hoped he wasn't coming down with anything. Lord knew who would patch up Sheppard's team if he were out of it. He rolled over with the intention of getting something for his throbbing head and was surprised to feel cold floor under his fingers. That was odd. Had he fallen off his bed?

"Doc?" said a gruff voice to his left. "You okay?"

"Ronon, lad," Carson answered sleepily. "What are ya' doing in my quarters?"

"This isn't your quarters," came the tense reply.

Carson frowned and tried opening his eyes. At first, he was grateful for the dim light. Then his vision focused on his surroundings. The pale bluish lights illuminated a small circular room with ribbed walls. The frighteningly familiar pattern was broken only by an opening blocked by a latticework of web. He sat up quickly and immediately regretted it when his head protested. Ronon steadied him with a strong hand.

"You okay?" he asked again.

"Okay?!" Carson squeaked. "We're on a bloody Wraith ship!"

"Yeah, well," Ronon scratched his head, "beyond that."

Carson took a deep breath that did nothing to steady his heart, but managed to calm his voice. "Aye. I'll live." He looked over his companion, who was squatting next to him, and noted with concern the dark bruises that covered his limbs. "What about you?"

"I'm fine," he said dismissively.

"Ya' don't look it, son." Carson sat up straighter. "Let me take a look at you."

"I said I was fine!" Ronon insisted. He got up and started to pace the room like a caged animal. This turned out to be a mistake as Beckett noticed him limping.

The doctor sighed. "Yer not and you know it. Now, sit down and let me do ma' job."

Seeing the determined look on his face, Ronon relented. He sat back down and let the physician check his leg. Though he refused to admit it caused him any discomfort, at least it would keep the other man's mind off their predicament.

"What happened?" Carson asked as he tested the runner's ankle.

"Not sure. I was taking a walk and saw a Wraith in your room. I tried to stop him, but another one was behind me and I didn't have my gun," he winced as Beckett found a tender spot. "Must've been knocked unconscious."

"Well, you only have a mild sprain. Though you should keep off it as much as possible."

"That's something."

"What do they want with us?" Carson asked with rising fear.

"Whatever it is," Ronon told him earnestly, "it can't be good."

"Holy crap!" Panic was starting to set in. "How did I get involved in this?!"

"Hey." Ronon patted his shoulder reassuringly. "We'll get out of this. I've been in Wraith ships before."

"And what did ya' do then?"

Ronon shrugged. "I'm still here."

Further conversation was halted by the sound of foot steps echoing from down the corridor. Both men tensed and rose quickly to their feet. Ronon stepped protectively in front of his friend, ready to strangle anything that came at them.

Three Wraith, two guards and a long haired male, marched down the hall. The cage-like door slid open and the male, who bore a striking resemblance to the late Steve, moved forward to look them over. Ronon snarled at him. The Wraith rolled his head and pointed a corpse-like finger at Beckett.

The two guards surged forward, but Ronon blocked their way. He lashed out at one with an arm and managed to knock it back before the other slammed his head with its stunner. Ronon crashed to ground in a heap.

"Stop it!" Beckett shouted, stepping in front of the stunners now leveled at Ronon.

"Beckett," Ronon growled, trying to hint that the man should stay out of the the way.

"This isn't helping either of us, Ronon." Carson's voice was firm, but his eyes betrayed his fear. "I won't see you hurt protecting me."

Carson was led away before Ronon could leap up to stop them. He slammed his fist against the wall in fury and frustration. If anything happened to the little doctor, he wouldn't stop until every Wraith on this ship was dead. Even then, he wouldn't be able to forgive himself.

TBC...

AN: Muahahaha! Hope you enjoyed the chapter and thank you so much for your patience and happy reviews. It really means a lot to have so many people comment! Next chapter should be up much faster. Many thanks!


	4. Chapter 4

AN: This chapter has an appearance by Jamie. You don't have to have read my earlier stories to enjoy the scene, but if you like him I would recommend it.

Gene Warfare, by Rowana Farrin

**Chapter Four**

Beckett had to almost jog to keep up with his Wraith escorts. They passed through long corridors lined with web covered cocoons. Most were empty, but some still contained motionless forms or brittle husks.

Carson shivered. He sincerely hoped that that was not his fate. He wondered if Sheppard and Rodney were looking for him yet. He wondered if they would find him before he was a shriveled skeleton.

All too soon, the hall opened into a dark, oval room. The guards shoved Carson forward into the dimly lit center. He looked around the darkness wildly. The room was empty except for the guards, standing impassively by the door. Maybe he could rush them? No. He dismissed the thought. They would shoot him down the second he moved.

"Thinking of escape?" The voice was like honey and poison.

Carson froze. It felt as though the ice of Antarctica had been poured down his back. He did not dare to turn around and face the source of the voice. Unfortunately, he did not have to.

The female Wraith swanned into the light. She was beautiful, in an eerie, horrible way. Her corpse green skin was framed by a waterfall of gold and silver hair. Her golden eyes leered at his pale blue ones. Carson was starting to think he should borrow Rodney's idea and "pass out."

"Even if you could leave this room, you can not escape the hive," the silky voice continued. "Do not cause yourself unnecessary pain." She raised a clawed finger and ran it down his face. "You are the one called Beckett."

It was a statement, not a question, but Carson felt compelled to answer. "Aye," he croaked.

The Wraith smiled, showing far too many pointed teeth. "I have heard a great deal about you." She leaned closer. "You have knowledge that I require."

"I do?" Carson asked weakly. His throat was suddenly very dry.

"Yes," he Wraith answered with far too much pleasure. "You have the genes of our old enemy."

"Aye." There was no sense in denying it. It was clear this Wraith already knew.

"And you have given others of your kind these genes," she continued.

Carson stiffened even more. He didn't like where this was going. How much more did this Wraith know? What if there were Wraith ships headed for his home right now?

The queen backed away to circle him again. "Do not be distressed. We simply want you to give us what you gave your people. In exchange, your lives will be spared."

Carson's mind worked frantically. He was terrified out of his wits, but he was not fool enough to give Wraith control of Ancient technology. Even if she was telling the truth about letting him live, which he sincerely doubted, the cost was too high.

It took him three tries to get his trembling tongue to obey him. Finally he got out: "No way in bloody hell!"

The queen snarled and slapped him to the floor. The guards came forward and picked him up roughly by his arms to face her again.

"You have until tomorrow to change your mind," she growled dangerously. "If you have not, I will feast on your friend every day until you do. Such a strong one is a rare treat." With that, the guards dragged Carson back down the maze of passages to his cell.

--------------------

McKay rubbed his eyes and glanced up at the clock. It was 6 AM and he was no closer to finding the Wraith ship than when he'd started, five hours ago. He reached for his mug and was distressed to find it empty. Frustrated with his own inability to find a solution, he left. He decided a walk might clear his head. He wandered the hallways in the general direction of the mess hall, his mind lost in a maze of equations and simulations.

He looked up and found himself in front of a familiar door. He sighed. Might as well do something for his head while he was here. He palmed the door open and wandered into the quiet infirmary. The stillness was unnatural. Rodney was used to seeing Carson busy with one thing or another and his absence made it seem hollow.

_'Mommy!'_

A streak of green launched itself at McKay's leg and proceeded to climb up to his shoulder. McKay shouted in surprise and started desperately trying to shake the creature off his arm.

"You rotten, green monster!" he yelled. "I am not your 'mommy'!" He danced around like a madman on hot coals, vainly swatting at the clinging animal.

"Is that you, McKay?"

_Oh, great_. He moaned, _just when it couldn't get any worse_... Lt. Cadman poked her head out of Carson's office. She had to cover her mouth to keep from laughing at the ridiculous scene.

"I guess Jamie likes you," she said, when she could control herself.

In response, the sea dragon bit McKay's arm. McKay howled and flung him to the floor. The lizard slunk over to Cadman.

_'Meany'_

"Thanks for realizing," Rodney hissed through clenched teeth. Not for the first time, he wished he hadn't activated the cursed device that let him understand the dratted creature. Or that the device hadn't burned out, preventing others from sharing his misery. Although Carson would probably have enjoyed knowing what his pet was thinking.

Cadman bent and let Jamie climb up her arm. "Silly, Jamie," she crooned. Then, she looked back to McKay. "I was about to feed him. Any luck finding the Wraith?"

"Not really," he replied sadly.

Cadman looked disappointed, which was an understatement to how she really felt, but the military personal learned to hide their feelings. "You know, you may be the answer man, but that doesn't mean you have to do everything yourself."

McKay opened his mouth to retort, but Cadman had moved into Carson's office. He decided he was too tired to bother about her now. He knew she was just as worried about Beckett and Ronon as he was, even if her presence still made him squirm.

_'Hungry!'_ Jamie's cries echoed in McKay's head. He shook it and turned back to the door. He wasn't making any progress standing around here.

Cadman reappeared with a bowl of small fish in one hand. Jamie sat on her arm, greedily snatching fish from it. He glanced up at McKay and hissed.

_'Meany'_ he declared again.

Rodney glared back. "If I'm such a 'meany,' how can you ever mistake me for Carson?"

_'Same legs.'_

"Half of Atlantis has the same legs," Rodney snorted. "How do you tell us apart?"

_'Meany stinks.'_ Jamie returned to his feast.

McKay stared. It was the first time Jamie had given any indication that he understood him. More importantly, the little wretch had just giving him an idea, one that might solve the problem of finding the Wraith in time to save Carson and Ronon.

Cadman was watching McKay with concern. She was beginning to wonder if the stress had finally caught up with the man. Then, he turned and dashed out the door. Cadman ran after him, still holding Jamie and the bowl. "Where are you going?"

"To find Carson and Ronon!" he yelled back, before disappearing around the corner.

Minutes later, Weir had gathered most of the command personnel in the briefing room to hear McKay's plan. McKay himself arrived last, laden with his laptop and looking much happier than the past few hours.

"I take it you have some good news for us?" Elizabeth asked expectantly.

"Better news!" McKay announced.

"Better?" Weir raised an eyebrow questioningly. "I like the sound of that."

Without waiting for more questions, McKay launched into lecture mode. "I have been able to identify the hive ship where I believe Carson and Ronon were taken!"

"How?" Sheppard asked impatiently.

McKay raised a finger for them to wait and typed a few keys on his computer. A map of the Pegasus Galaxy appeared on the large wall screen. "These," McKay pointed to the scattered red dots on the map, "are Wraith hive ships within range of the city's deep-space scanners."

"That's a lot of dots," Sheppard remarked.

"I know," McKay admitted. "It's almost impossible to distinguish between them at this range. Essentially, they all emit the same sub-space signals."

"How does this help us find Carson and Ronon?" Weir asked.

McKay grinned. "Watch this." He type a few more keys. Suddenly, all the red dots disappeared except for one located about half way between Atlantis and the edge of the map. The crowd of people in the room looked at it with surprise.

"What did you do?" Zelenka asked, feeling slightly miffed at being left out of his colleague's discovery.

"Almost the same thing you did before," he admitted. "I modified the sensors to identify Ancient targets as well as Wraith."

"But the sensors still say it's a Wraith hive ship," Col. Caldwell pointed out. "How is this one any different from the others?"

"Didn't I just say it was identifying Ancient signals as well?" McKay said impatiently. "Based on the fact that these Wraith were using Ancient signals to disguise their ship, it's conceivable that they used the same type of modifications on their Hive ship."

"Then, why does it not show up as Ancient on the sensors?" Zelenka asked.

"I don't know!" McKay replied, exasperated. "Maybe the modifications didn't work on something that large or maybe they haven't finished yet. What I do know is that it gives this Hive ship enough of a differences in its signature to identify it at long range."

"How long will it take the Daedalus to reach it?" Sheppard asked.

"At maximum speed, four hours," Caldwell told him. "We can be ready to go in ten minutes." He was already on his radio, ordering the vessel prepared.

Sheppard turned to Weir and opened his mouth, but she was already ahead of him. "You have a go, Colonel. Just be careful."

He nodded. "McKay get what you need and be ready to leave in five minutes. Teyla, Lorne, and Cadman; you're with me. We're going to get a couple of jumpers, just in case."

People scattered so quickly that the room was soon empty of nearly everyone but Weir and Caldwell. The military commander regarded her warily. "You realize that Ronon and Dr. Beckett may have seriously compromised this location."

"I think you underestimate them, Colonel," Weir replied tersely.

"I have every respect in both Dr. Beckett and Ronon Dex, Doctor," he stated with the air of one reopening an old argument. "But the good doctor isn't my first choice for resisting interrogation." He gave her a firm look and added, "this isn't going to be a rescue mission. We need to eliminate that Hive ship before the information spreads to the other Wraith."

"I'm aware of that, Colonel," Weir affirmed, equally firm. "But, I also trust you to remember that I am responsible for all the lives in this city and that includes Ronon and Dr. Beckett." Her eyes narrowed in determination. "And we will not give them up without a fight."

TBC...

AN: Will this plan work? Or will the Wraith out smart them again? The next couple of chapters should be pretty exciting! I had some difficulty with this chapter, so your thoughts are greatly appreciated. Many thanks, as always, to my wonderful reviewers! You guys are great! I'll try to keep updates pretty regular for you.


	5. Chapter 5

Gene Warfare, by Rowana Farrin

**Chapter Five**

Ronon turned for his hundredth and something pace around his cell. He hated waiting. The Wraith had brought Beckett back and dumped him on the floor. Since then, the doctor had barely said two words. He just sat in a corner staring off into space. Ronon had tried to start a conversation a few times, but had given up long ago. He wasn't much for talking anyway.

After five long strides, Ronon reached the far wall. This time he slammed his hand into it with such force that he could feel his knuckles bruising. Beckett jumped and stared at him, actually looking at him for the first time in hours.

"Sorry," Ronon mumbled. He squatted back to the floor and tried to meet the other man's gaze, but Carson avoided his look. Ronon sighed and leaned back against the wall.

Finally, Carson broke the silence. "How do you do it?"

"Do what?" Ronon asked, hiding his relief at hearing the doctor speak.

"Stand up to them."

Ronon shrugged. "I do what I have to."

Carson was quiet for a moment. Then, "They want me to give them control of Ancient technology."

Ronon made a noncommittal noise.

Carson went on. "If I do that, they'll take Atlantis for sure."

Ronon looked at him. "So don't."

Carson was avoiding his eyes again. "If I don't, they'll kill you."

_Oh_, Ronon thought, _so that was why he'd been so quiet_. "They'll probably kill us both eventually," he pointed out. "At least then they won't get what they want."

Carson sighed and stared at the ceiling as if it could solve his problems. "I don't think I can watch that."

Ronon frowned at him. He really didn't have much to say to that. He had never spent enough time with the good doctor to really get to know him. Though, from what he did know, he knew that Beckett would do anything in his power to save the lives of other people. In a way, Ronon supposed, they weren't that much different. Before his years of running, Ronon had done his best to defend those around him. Now that he had found these people, he was determined not to fail them the way he had his own.

Before he could think of what to say, the stomp of footsteps heralded the return of their captors. Both prisoners stood and Ronon gave Carson a reassuring glance before the cell door slid open. Steve's twin was back with more of his minions. This time, Ronon didn't try to stop them when they came into the room. He wanted to save his strength for the right moment. That, and there were at least seven Wraith this time, which was more than he thought he could handle on his own barehanded at least.

The Wraith shoved the two down the halls until they reached the room where Carson had been interrogated hours ago. The Queen was already there, eyes gleaming hungrily, and looking all too pleased to see them. Two guards continued to restrain Ronon while the rest stood at attention. The Queen stalked forward to caress Carson's cheek with a finger. Ronon struggled with his guards, but to no avail.

"I hope your mood has improved," the Queen leered.

Carson took a deep breath. "Listen," he said, trying his best to keep his voice from shaking, "even if I agree to help, I'm not even sure it can be done."

The Queen moved past him to look over Ronon. "I'm sure all you need is the proper motivation." She ran a long finger down Ronon's chest, while the big man glared at her.

"I didn't say I wouldn't try!" Carson said desperately. Ronon gave him a warning glanced, but he ignored it.

"Oh, I believe you will do more than try," the Queen crooned, not taking her eyes off of Ronon.

Carson jumped forward in panic, but two of the guards blocked his path. Ronon snarled at the Queen, who just smiled nastily at him. Her hand traced lovingly along his torso. Without warning she leaned back and slammed her right palm into his chest.

Someone screamed, but it wasn't Ronon. It was Carson. He tried to fight past the Wraith guards, but it was hopeless. "Stop it!" Carson's voice was panicked. Though he was praying that she would, his frantic mind didn't think it would happen.

Carson was surprised when the Queen paused in her feeding. Her grin of enjoyment faded into a frown and she withdrew her hand. Ronon grunted in pain and staggered, held up by the Wraith guards. With the Queen distracted, Carson pushed forward and steadied him. The guards, who had perviously restrained him, watched unconcerned.

Ronon's eyes were half shut and his teeth clenched against the pain. Carson was impressed that the man hadn't passed out yet. He looked him over quickly and was relieved to find little signs of aging, the feeding must not have been long enough to show lasting effects. Even so, Ronon looked terrible and desperately needed medical attention.

The Wraith Queen seemed to be conferring with her lead guard. It was hard to tell, since they weren't actually speaking to each other. Then, she turned to Carson and gave him another of her horrible smiles.

"Your friends are persistent," she told him. "Even now, they seek to attack us with their primitive ship."

Carson's heart leapt. The Daedalus must be here! Sheppard and the others had come to their rescue, at last. Yet, even as he felt joy at the thought, he couldn't shake a nagging feeling of doubt in the back of his mind. The Wraith Queen hadn't seemed at all distressed by the Daedalus's appearance. In fact, she had seemed almost happy about it. Carson's mind failed to work out the significance of that, but he knew it could not be good.

---------------------

Sheppard paced the bridge of the Daedalus behind Col. Caldwell's chair. He knew it wouldn't make the four hour trip go any faster, but at least it let him vent some of his frustration. While on the ship, he was little better than a passenger, which meant he didn't have much do. He hated not doing anything.

"You can stop wearing holes in my ship, Colonel," Caldwell informed him. "We're almost there."

"Finally!" He moved over the wall that held the ship's scanners. A large red dot was in orbit around the system's second planet.

"We'll come out of hyperspace here," Caldwell said, coming up behind him. He was pointing to a spot on the other side of the planet. "Then, you can take a puddle jumper and try to locate Ronon and Dr. Beckett."

Sheppard nodded. "McKay's working on adjusting the puddle jumper's sensors to scan the inside of the Hive."

"Good," Caldwell said with approval. "If you find them, radio back their location and we'll beam them out before we destroy the ship." He looked hard at Sheppard. "If not, we destroy the ship and get the hell out of here." His look dared Sheppard to protest.

Sheppard just scowled at him and didn't answer. He knew they had to destroy the Wraith Hive one way or another. He didn't want to think about doing it with his friends still on board. He turned and headed down to the hanger, radioing for McKay and Teyla to meet him there.

They were ready in the jumper when the Daedalus came out of hyperspace a few minutes later. What they weren't ready for was the wave of Wraith darts waiting for them on their approached.

Sheppard heard Caldwell bark orders over the radio as the ship veered to avoid the ambush. F-302s' were quickly manned and launched in an attempt to draw fire away from the ship, while Lorne and Cadman made for the second jumper.

"How did they know we were coming?" McKay asked in dismay.

Sheppard didn't bother to answer the question. Now was not the time. The hanger door opened and both puddle jumpers were out in the escalating battle. Sheppard spun his jumper to the right and fired two drones at an approaching dart. He was rewarded by a plume of red flames as the tiny craft exploded.

"At least these guys aren't immune to drones," he said happily. He fired three more shots that decimated another two darts.

"That's not what concerns me," McKay said from the back of the jumper. He was watching the battle tensely, his hands going white from clinging to the seat.

Caldwell's voice sounded over the radio. "The Hive ship is moving to intercept the Daedalus."

Sheppard frowned and the heads up display popped up to show the Hive ship moving around the planet in their direction. "Can the Daedalus hold out?" he asked.

"We'll be fine," Caldwell confirmed. "It's only one Hive. But if you want to find Ronon and Beckett, you had better go now. I'm not risking my ship any longer than necessary."

"On our way. Sheppard, out." He cloaked the jumper and turned towards the approaching Hive. "McKay, see if you can adjust those sensors."

"Working on it," McKay called from the back, already engrossed in his work.

Teyla was eyeing the large Wraith vessel as it loomed into view. She could feel the Wraith presence in the back of her mind, but it was different from what she expected. She leaned over to the pilot seat. "Something is wrong."

"What?" Sheppard asked, without taking his eyes off the screen.

Teyla shook her head to clear it. "I am not sure. These Wraith...are not distressed that we are here."

John turned to look at her. "What does that mean?"

"I do not know," Teyla admitted, but she was unnerved nonetheless.

Sheppard frowned, equally disturbed. "McKay, are we close enough for those sensors, yet?"

"Almost..." McKay called. "Oh, no." he added quietly.

"What?" Sheppard snapped. He was not in the mood for more bad news.

"I'm reading massive power fluctuations coming from inside the Hive ship."

"How massive?"

McKay swallowed. "Large enough to be a ZedPM."

Sheppard stared at him. "The Wraith have a _ZPM_?!"

"Or something equally as powerful, though given that these Wraith seem to like Ancient technology..." he trailed off. "I mean, this could be really, really bad."

"Sheppard, the Wraith Hive ship is now in range," Caldwell said over the radio. "What's your status?"

"Get those sensors working." Sheppard ordered before tapping the controls to respond. "We haven't located Ronon or Beckett yet, but McKay thinks the Wraith may have a ZPM on board."

"Is he sure?" came the skeptical response.

"Pretty sure," Sheppard confirmed. "I doubt the Wraith have the technology to make use of it, but I wouldn't put it past them."

"Understood. How much more time do you need?"

"It'll only take me another minute to reconfigure the sensors," McKay called from the back.

"Fine." Caldwell agreed. "Keep in touch. Caldwell, out."

Teyla was watching the screen with concern. "What's wrong?" Sheppard asked.

"Why has the Hive not attacked the Daedalus? They are well within range."

Sheppard frowned and glanced at the heads up display. Teyla was right. The Wraith should be within range of the Daedalus. Why weren't they firing?

---------------------

Carson watched the Wraith Queen in apprehension while he did his best to treat Ronon. It bothered him that she was so unperturbed by the whole situation. Ronon suppressed a hiss as Carson held a makeshift bandage to his bleeding chest.

"Sorry," Carson apologized. He lessened the pressure a little. "How are ya feeling?"

"I'm fine," Ronon said gruffly. "Don't worry about me."

Carson smiled. The man had lost none of his nerve. A shadow passed over them and Carson looked up to find the Wraith Queen leering down at them. "Come with me."

They didn't have a choice. The Wraith guards soon manhandled them both into walking behind their Queen. Ronon was unsteady on his feet, but given the circumstances, was holding out fairly well. They were led through more of the maze of halls to a large, unfamiliar door. The lattice and web were dark, making it impossible to see what was inside.

The Wraith Queen grinned wickedly at them before opening the door. The room was much like the one they had just left, but larger. The center, however, was not empty. Carson stared in absolute shock and horror.

The Wraith had a Control Chair.

TBC…

AN: Hehehe. I am evil. Hope you enjoyed that as much as I liked writing it. Please don't forget to review! As always thanks to those who did leave me comments! And thanks to my beta readers again! They're the best!


	6. Chapter 6

Gene Warfare, by Rowana Farrin

**Chapter Six**

Colonel Caldwell eyed the looming Hive ship with apprehension. It hadn't moved for the past few minutes, it just sat there while the darts mounted sporadic attacks on the Daedalus. Caldwell didn't like it. They had to be up to something. He leaned forward in his chair.

"Be prepared for hyperspace at a moment's notice," he ordered.

"Yes, sir!" the young helmsman replied. Steven smiled. He like the man, Kleinman was his name. He knew how to be calm in a crisis. Caldwell was confident that all his men would perform well under any circumstances and this was no different.

The radio crackled into life and McKay's voice came through. "I think you should see this, Colonel," his voice was nervous, which was never a good sign.

A data burst came through from the puddle jumper and Caldwell nodded to have it put on the screen. A rough schematic of the Hive ship appeared with several scattered dots and signals.

"So, you got the sensors working," Caldwell noted. "What am I looking at?"

"The large yellow dot near the center is the large power source I'm reading."

Caldwell leaned forward, eying the smaller white dots around it. "Are those Wraith surrounding it?"

"Yes," McKay confirmed. "Except for the green ones."

Caldwell now saw two green dots in the midst of the white ones. His eyes narrowed as realization dawned. "Are those Dr. Beckett and Ronon?"

"That's a fair guess," Sheppard confirmed. "Can you get them out?"

"Stand by." Caldwell tapped the ships intercom. "Dr. Novak, can Hermiod lock onto the two points inside the Hive ship?"

There was a pause, then, "Hermiod says that the odd power fluctuations in the room are interfering with the transport."

Caldwell sighed. "Can he still beam a warhead inside?"

"He says he'll have to make some modifications first to transport in or out," Novak replied. "And he doesn't seem happy about it."

When was the Asgard ever happy? "Just do it," Caldwell ordered.

Caldwell tapped the radio again. "Sheppard, we need to make some modifications to the transporters. What's the status on the Hive?"

"Nothing," Sheppard replied in frustration. "Still not moving."

Caldwell's frown deepened. "Divert all power to the shields," he ordered. Whatever the Wraith were up to, he was determined not to be caught off guard.

---------------------

Carson stared at the Chair. His frozen mind refused to accept that it could be here, but he could not deny what his eyes were seeing. It looked just like the one on Atlantis, blue with ribbed silver bands and wide armrests. It was sitting on a small platform in the center of the room. He had never liked the times he had been forced to use the device, but now he was more afraid of it than he had ever been.

"How...?" he stammered to no one.

"We have been studying Lantean technology for centuries," the Wraith Queen answered. She moved forward and stroked the Chair lovingly. "Many of their systems have been successfully integrated into our ship and weapons." She walked back to regard him again. "But our scientists have been unable to produce the gene that would allow us full control of the technology."

"This is bloody insanity!" Carson shouted at her. "That's why you want the gene therapy!"

The Queen smiled. "Yes. Though, at the moment, I have a different task for you." She leaned closer until her face was inches from his. "You will control the Lantean weapons for us."

Carson's eyes widened. "Are you mad?! I can't do that!"

"You can. And you will."

"You can't make me attack my friends!"

She smiled again and turned to Ronon, who had been glaring at her behind her back. "I think I can."

Carson's mind raced. "If you feed on him again now, you'll kill him!" His voice was getting high and panicky and he fought to keep it under control. This was starting to be too much for him to handle.

Ronon growled at the Wraith who had moved forward and wrenched him upright again. Carson was pulling at the ones who were holding him. The Queen just grinned at him and reached forward with her hand.

"Stop!" Carson cried. "Stop. I'll do it."

Ronon turned his glare on the doctor, but the man was avoiding his glance again. The Wraith shoved him towards the Chair and he sat down reluctantly. He felt sick and sincerely hoped he would have the control necessary to keep from destroying the Daedalus.

"I'm warnin' you," he told the Queen. "I'm not good at this. I could kill us all."

"I am sure you will perform adequately," she declared, not moving from her position next to Ronon.

The threat was clear. Carson took a deep breath and leaned back. The chair glowed into life. _I hope I'm doing the right thing_, Carson prayed.

--------------------

Sheppard watched the dots on the jumper's screen that represented his friends. He wished he had a way to see what was happening in there. It was so frustrating, sitting here, unable to do more than watch. At least none of the dots had disappeared.

"Colonel," McKay called. "I'm reading massive power surges moving through the Wraith ship."

"What does that mean?"

"I don't know," McKay admitted, frowning at the screen. "But these power readings are Ancient, not Wraith."

"Ancient?" Sheppard asked, confused. He reached for his radio with the intention of warning the Daedalus. Then, he froze. Dozens of golden missiles were flying from the bowls of the Hive and heading straight for the Earth vessel.

"Those had better not be what I think they are!" Sheppard shouted angrily. But the jumper's scanners confirmed it. They were drones. It just wasn't fair.

"No way!" McKay was staring in dismay.

"Colonel, you have incoming!" Sheppard shouted over the radio.

"We see it," Caldwell acknowledged. "We can't maneuver with all the darts. I'm recalling the F-302s. I suggest you make your way back, too. We may have to leave in a hurry."

"We can not leave without rescuing the others!" Teyla argued.

"We can't do anything from here," Sheppard reminded her. "We need to get back to the Daedalus."

He turned the jumper and started to head back into the fray. The space around the Daedalus was so full of darts and drones that it was impossible to get near.

"Hang on!" Sheppard told his passengers.

He decloaked the jumper and fired several of his own drones to clear a path. It worked up until they were half way to the hanger doors. Two darts broke off their attack on Daedalus for the smaller target. The jumper shook as several shots found their mark. Sheppard tried to cloak the jumper again, but nothing happened.

"We are so dead!" McKay cried in panic.

"Shut up!" Sheppard shouted back. "Try to get the cloak working again."

"Sheppard, you have two more darts at 12 o'clock," Caldwell radioed from the Daedalus.

"Great," Sheppard's voice was rich with sarcasm. He fired more drones, but only managed to take out one of the approaching darts. That still left three closing in on them.

"Damn it!" Sheppard swore. He leaned as he tried to swerve away from the darts. It didn't help. The kamikaze Wraith were headed right for them. Sheppard closed his eyes as the world exploded in a ball of fire.

John squinted his eyes open again. The darts were gone.

"Ok," he said, relaxing slightly, though very confused. He turned the jumper back towards the Daedalus.

McKay peeked from the back. "We're not dead?" he asked in disbelief.

"So it would seem," Teyla confirmed, equally relieved.

"What happened?" McKay asked.

Sheppard glanced at the sensor readouts on the screen. "The drones," he said. "From the Wraith ship, they attacked the darts."

"You sure that wasn't you?" McKay asked.

"Positive." He glanced back as the jumper eased into the hanger. "Friendly fire?"

McKay frowned. Then, his face lit up as it dawned on him. "Carson! He must be controlling the drones."

Sheppard's face hardened. "They're making him fire drones?!" he asked angrily.

"It's the only thing that makes sense," McKay said reluctantly. "If they could control the drones themselves, they wouldn't need him in the first place."

Before the full implication of this could sink in, the Daedalus shook violently.

"Let's get to the bridge," Sheppard decided.

The three took off down the ship's corridors, dodging rushing crew members as they went.

--------------------

Caldwell clung to the arms of his chair as his ship shook again. A steady stream of drones was no impacting the Daedalus's shields. It was clear the ship could not hold out much longer.

"Status report?" Caldwell asked.

"Shield strength is dropping rapidly," Kleinman reported. "At this rate, the shields will fail in less than two minutes minutes."

"Are all the F-302s and jumpers aboard?" he questioned.

"Yes, sir. Colonel Sheppard's jumper just came in."

"Good. Prepare the ship for hyperspace on my mark." After the young man nodded, Caldwell tapped the radio on his chair. "Dr. Novak, what's the status on that transporter?"

The ship gave another violent shake before the woman's nervous reply came through. "The increase in the power fluctuations is making it difficult to compensate. Hermiod says it will take a few more minutes."

"We don't have a few more minutes!" Caldwell snapped angrily. So much for Plan A. "Shields are failing!" came Kleinman's urgent cry.

Before Caldwell could react, the whole front console exploded as the ship rocked wildly. Several crew members were shaken off their feet as Caldwell clung to the arms of his chair. His nose smelled the tang of burning flesh as people rushed to put out the various small fires around the room.

"Get us out of here now!" Caldwell ordered, trying to stop the ringing in his head.

When nothing happened, he glanced to his side and saw Kleinman sprawled half in his chair and half on the floor. Blood was pouring from a wound on his left temple and his right arm looked charred.

Caldwell cursed. "I need a medical team on the bridge!" he shouted. He got out of his chair and checked the man's pulse. Weak, but present. He let out a breath.

The medical team arrived with Sheppard, McKay and Teyla on their heals.

"What happened?" Sheppard asked at once.

"We lost our shields," Caldwell informed him. He stepped back so the medics could tend Kleinman. Turning to one of his other men, he asked, "What's our status?"

"Numerous casualty reports from all decks," the man replied. "Life support is still functioning, but we've lost primary sub-light engines."

"What about the hyperdrive?"

"Still functional."

"And the hive ship?" Sheppard asked.

"It's stopped," the man said in confusion.

"Stopped?" Caldwell repeated.

"Yes, sir. It's not firing drones anymore."

"Why would they do that?" Caldwell asked.

"Because Carson's controlling the drones," McKay announced.

Caldwell rounded on him. "Are you telling me that Dr. Beckett's the one who's been attacking us?"

"He probably doesn't have much of a choice," Sheppard pointed out. "He must be trying to give us the chance to escape."

Caldwell still looked unconvinced, but he nodded. "Let's not waste it. Take us to hyperspace," he ordered.

"But we can't leave them in there!" McKay protested.

"Doctor," Caldwell said with little patience, "My ship is falling apart, my men are injured, and I, for one, am not willing to risk losing this entire crew a second longer!"

The ship turned and launched into hyperspace, leaving the Hive ship behind.

"I'm sorry," Caldwell added to all of them.

"Yeah," Sheppard agreed. "I'm sorry too."

------------------------

Sharp pain pulled Carson back to his body. He was yanked forcefully from the Chair and thrown onto the floor. He clung to his arm where the Queen's claws had left a trail of blood. Then she had him by his neck and was pulling him upright. He clung to her arm as his feet dangled above the floor, trying desperately to keep from suffocating. He could hear Ronon's shouts and struggles in the background, but couldn't turn to look.

The Queen was livid. Her eyes burned with an anger that bore into his soul.

"How dare you defy me!" the Queen shrieked.

Carson didn't have enough breath to answer. He was starting to see spots and knew he couldn't hold on much longer.

"He did what you asked!" Ronon shouted. He was gaining strength, even as Carson was losing his. "You still need him alive!"

The Queen's anger seemed to subside a little, but she did not loosen her grip. She hissed dangerously and drew Carson closer to her.

"This will not go unpunished," she growled. "When we have control of Lantean technology, your world will be the first that we cull."

She dropped him in a heap on the floor, where he lay gasping. At an unspoken signal, the Wraith guards moved forward to take both him and Ronon back to their cell. As he was half dragged down the hallways, Carson couldn't help but think that he had doomed all of Atlantis. He was beginning to wish the Queen had killed him after all.

TBC…

AN: Hooray! We've reached the halfway mark! Some parts of this chapter were a little tricky, especially the technical bits, so sorry for any mistakes! Kleinman whumping was put in for my beta reader Nalana. Always keep your beta readers happy! Please leave thoughts, complaints, or praises; I do pay attention to them. Many thanks as always! I will try to have chapter seven by the end of the week.


	7. Chapter 7

Gene Warfare, by Rowana Farrin

**Chapter Seven**

Elizabeth watched from her favorite balcony as the Daedalus landed on the Atlantis pier. Even from here, she could see the damage the Wraith attack had done. Parts of the ship's haul were shorn away and blackened by fire. Even though Colonel Caldwell had reported no fatalities, it seemed like a miracle that anyone could have survived such an assault. The sight made the truth of what had been reported to her sink in; the mission had been a failure.

Colonel Caldwell came up behind her, looking more subdued than she had ever seen him. Despite their various confrontations, Dr. Weir had come to respect him as an officer and a leader. Seeing him in this saddened state distressed her.

"How's Lt. Kleinman?" she asked politely.

"He's going to be fine," Caldwell answered. "Thank you for your concern."

She nodded and turned back to look out at the vast ocean.

"I'm sorry," Caldwell stated.

"It's not your fault," Weir countered. "At least we know they're alive."

An uncomfortable silence followed. They both knew that being alive in a Wraith ship was almost worse than being dead. The chances of seeing either Ronon or Carson again were small.

"Dr. Weir!" Zelenka called urgently.

Elizabeth moved back into the operations area with Caldwell right behind her.

"What is it?" she asked quickly.

"The Wraith," he pointed at one of the Ancient screens. "They're headed for Atlantis."

"How long untill they get here?"

Zelenka shrugged. "Three weeks, maybe four. They aren't moving as fast as we've seen."

"Taking their time," Caldwell observed. "How many?"

"That is just it," Zelenka said, confused. "There is only one."

Caldwell frowned. "Just one?"

"Yes. According to the scanner, the same one that took Ronon and Beckett."

"Are you sure about that?"

"Yes," Zelenka pushed his glasses up his nose. "It is definitely the same one."

"Alright," Weir accepted. "Get everyone together. We need a plan."

Once again the briefing room of Atlantis was filled with all the chief scientists and military personnel. Dr. Weir calmly explained the situation to the assembled people and then put out a call for ideas. Instantly the room was a cacophony of noise as scientists and soldiers began squabbling amongst themselves about the best way to defend the city. Elizabeth let them go on for a minute before cutting into the conversation.

"That's enough!" she shouted, keeping her voice level. "I said I wanted ideas, not arguments." The room fell silent once more. "Thank you. Now, let's get started. Last time we were able to defend the city against three Hive ships. We must have some idea of how to do it again."

"Last time the Wraith didn't have an Ancient Control Chair and the means to use it," McKay interrupted. "Who knows what other Ancient technology they could be using! This is a disaster!"

"Why?" Weir asked patiently.

"The problem is, the shield is designed to allow the Ancients to defend Atlantis," Zelenka explained. "It is programmed to allow drones to pass through it to attack enemy ships."

"Alright," Elizabeth said. "Can you fix it?"

Zelenka opened his mouth, but McKay cut him off, "Of course I can fix it," he said, as if it were obvious. "But, if we override the Ancient codes allowing drones to pass through, we won't be able to attack either."

"Stalemate," Sheppard observed.

"Until we run out of power and this entire city is destroyed!" McKay added.

Weir nodded understanding and turned to Col. Caldwell. "How long will it be before the Daedalus is repaired?"

"The damage was more extensive then we first realized," Caldwell said regretfully. "The sheild generators are completely shot and life support is barely functional. Even working around the clock, it's going to take my people at least a month to repair the damage."

"I can offer you personnel from Atlantis to assist with repairs," Weir suggested.

"As much as I appreciate the thought, Doctor, it won't be enough. The Daedalus won't be ready to fly by the time the Wraith get here, much less fight a Hive ship."

"Excuse me for interrupting," Sheppard jumped in. "But aren't these Wraith being a little overconfident, coming at us like this? I mean we took out four of them last time they tried this."

"Last time they didn't have a ZPM and an arsenal of Ancient drones," McKay pointed out, annoyed at having to repeat this fact.

"What's your point, Colonel?" Caldwell asked.

"My point is, I wouldn't jump into a fight like this unless I was sure I could come out on top."

Weir raised an eyebrow. "You're saying there's more to it than what we've already seen?"

"I'm just saying," Sheppard said firmly, "that they caught us off guard once and I'd rather not give them the chance to do it again."

"Alright." Elizabeth scanned the faces around the room. "McKay, I want you and Zelenka to head up work on the shield modifications. Sheppard and Teyla, I'd like you to organize the evacuation of the mainland and all unnecessary personnel to Earth or the Alpha Site."

As people around the circular room began to nodded, she addressed Caldwell. "Colonel, I'd like anyone you can spare to work on modifying the Daedalus's transporters."

"Why? The ship won't have enough sheild strength to last outside Atlantis."

"Let's just say, I'm not giving up on Ronon and Carson just yet."

-------------------

Carson rubbed his sore neck and gave a sigh. The Wraith had left them alone for the past few hours except to bring them dinner. The food had been surprisingly good, though Carson had avoided the meat. Not that he thought that the Wraith would serve them other humans, but he just wasn't sure he could stomach eating what had once been another living thing without thinking of what the Wraith were inevitably going to do to them.

Ronon was sitting across from him, eyes closed and head leaned back against the wall. Carson knew he wasn't actually sleeping. Neither of them had gotten much actual sleep since they had arrived here. Carson was still worried about possible side effects from the Wraith feeding, but the big man insisted that he was fine and dismissed any concern. He already looked mostly recovered, which was more than could be said for Carson's neck.

He was about to lean back and attempt to sleep himself when Ronon's voice broke the silence. "Are you really going to help them?"

Carson sighed again. "Aye. It doesn't seem as though I have much choice."

"Can't you just fake it?" Ronon suggested.

"I wish I could," Carson admitted, "but these Wraith are smart. They'll notice if I'm not doing anything. Though to be honest, I don't know if I can do it anyway."

Ronon leaned forward and lowered his voice. "What about giving them something else?"

Carson frowned. "What did ya have in mind?"

"You've been working on how to make them human, right?"

Carson's eyes widened. "Aye, but you saw what it did to Elia!" he protested. "You want me to turn them all inta monsters?!"

Ronon shrugged. "At least then they wouldn't be able to use Ancient technology."

"Aye," he agreed. "And we unleash hundreds of the beasts across the galaxy!"

They fell silent again. Carson mused over Ronon's idea. It would never work. Even if he wanted to do it, he didn't have any of his research materials here and it would be next to impossible to start from scratch. He needed a better plan. One that was slow enough that the Wraith wouldn't suspect what was happening.

He stood up as a sudden thought came to him. "There might be a way to..." Before he could finish, the Wraith guards returned and once more took him down the maze of corridors to see the Queen.

This time they took him to room cluttered with tables, shelves, and scientific apparatus the likes of which Carson had never seen before. It was surprising to see something so similar to his own lab on Atlantis in a Wraith ship. Though it was obvious the Wraith must have such rooms, with his limited view of Hive ships, Carson had never imagined they would have a room so normal looking.

The Queen was standing with a white-haired male near the center table. On it were clear vials and a device that looked like the Wraith version of a microscope. The Queen smiled at him in a way that displayed all her teeth, a painful reminder of what was probably in store for him.

"You will now begin work on the gene manipulation," she declared.

Carson took a deep breath and tried to steady his nerves. "You realize that with nothing to go on, it'll be virtually impossible for me to recreate the gene therapy, much less modify it for your people?"

The Queen smiled again and picked up a glass vial from the table. A vial containing a disturbingly familiar liquid.

"I believe this contains a sample of your work," she said with supreme confidence.

Carson felt sick. The vial contained human blood. "Where did you get that?"

"We captured one of your off-world teams," she explained, clearly taking great pleasure in his discomfort. "They were not forthcoming with information. But, we were able to _extract_ something useful from them." She waved a dismissive hand and grinned even wider.

Carson swallowed, but the lump in his throat would not go away. He remembered the team who had disappeared on a routine trading mission several months ago. Carson tried not to think about the way they must have died.

The Queen gestured to the Wraith beside her. "He will assist you with anything that you require," she said, in a way that made it clear he would also be watching Carson like a hawk. "I expect results in twenty-five days."

"Twenty-five days?!" Carson squeaked in panic. "I cannae do it that fast!"

The Queen leaned close and glared nastily. "I am sure I can find ways to motivate you."

She stalked out of the room, leaving Carson alone with the white-haired Wraith. Carson sighed and rubbed at his tired eyes. One thing was certain, he was going to have to learn to get some sleep in this place, assuming they were going to let him sleep. He glanced over at his Wraith guard, who stood watching him impassively.

"So what do I call ya?" he asked politely.

The Wraith growled at him. "You are not worthy to call me anything, human!"

"Touchy," Carson observed. He would have to learn not to push the Wraith too far, though he was fairly certain he was safe as long as he remained useful. His mind wandered to Sheppard's silly insistence on giving the Wraith Earth names. "How about George?" he asked.

The Wraith hissed, but when he gave no further protest, Carson settled on George. The familiar name helped somewhat to ease his fears. He turned to the table of vials and took a deep breath. Time to get started.

As the days passed, Carson soon grew accustom to the routine forced upon him. He would work for hours on end in the lab with George, then be taken back to the cell he shared with Ronon. They would be fed and allowed to sleep for a few hours before Carson would be put back to work again. Carson soon grew exhausted by the regime, but Ronon was almost going mad with boredom and inactivity.

He had recovered quickly from the Queen's brief feeding, but with no outlet for his energy and frustration, had taken to having boxing matches with the walls to release his anger. Only Carson's insistence that they were better off waiting than trying to escape prevented Ronon from attacking every Wraith he saw. He knew full well that they didn't have a chance of escaping the Hive while it was traveling. The Wraith ignored him for the most part, for which he supposed he should be grateful, but it just made him more angry. Angry at Carson for giving in to them. Angry at himself for being the reason. And angry at the Queen for planning the whole thing in the first place.

Carson worked as fast as he could, hoping the Wraith would not notice the slight changes he was making to the retrovirus designed to deliver the ATA gene. He had no chance of recreating the retrovirus he had been working on to make them human, but if his plan worked, it would be far more effective. Unfortunately, he had no way to test it until the time came. And if it failed, he would have doomed not only himself, but probably all of Atlantis.

Days turned into weeks and the Wraith Hive drew ever closer to Atlantis. A battle was dawning that would not soon be forgotten.

TBC…

AN: Well this was a difficult chapter to write. I would really appreciate some thoughts on it. Next time the action will pick up again. I like writing action. Sorry I didn't do much for Ronon; I promise he'll get moments later. Special thanks to all my faithful reviewers! I love you guys!


	8. Chapter 8

Gene Warfare, by Rowana Farrin

**Chapter Eight**

"And I'm telling you we would drain the power too fast!" McKay snapped angrily.

"Well, if you did not insist on opening such a small area at a time!" Zelenka countered.

"Anything larger and we'll be exposing ourselves to Wraith fire!" McKay protested.

"Only for a matter of milliseconds," Zelenka insisted, "hardly enough time to let anything pass through."

"What? And you want to take that risk?" McKay asked skeptically.

"Just because you are paranoid," Zelenka's temper was rising, " does not mean you can discount every idea I have!"

"Oh, please!" McKay snorted. "You haven't had a good idea since we've been on Atlantis!"

Zelenka threw his hands up and started spouting unintelligible swears in his native tongue.

"Woah there, Doc!" Sheppard had just entered the lab and seemed mildly impressed with the Czech's vocabulary. "I take it you guys haven't made any progress?"

"How am I to be expected to make progress working with people like these?" McKay asked, infuriated. Zelenka glared at him.

"I'll take that as a 'no'," Sheppard said in disappointment. He leaned closer, trying to see what was on the McKay's laptop.

McKay gave him an exasperated look. "Don't you have something better to do? Like polishing your gun or some other military nonsense?"

"Nope," Sheppard told him, still leaning over the scientists shoulder. "Nothing until our Wraith friends show up."

"Well, can't you do nothing somewhere else?" McKay implored. "We're trying to work here!"

"Sure thing, Rodney," Sheppard stood up straight and pointed at the screen. "That's wrong, by the way. It should be an area of 6.7 meters, not 7.2."

McKay gaped at him as the pilot turned and left the room. The inactivity of the past few weeks was getting to Colonel Sheppard. He itched to go after Carson and Ronon, but had been forced to wait impatiently for the ship to make its way to the city. It was infuriating. Even correcting McKay's math did little to lift his spirits.

"Sheppard?" A familiar voice came through his ear piece.

He tapped it. "Go ahead."

"Would you bring McKay and Zelenka to the briefing room please?" Dr. Weir asked. A brief pause followed and then, "They're here."

It was all she needed to say. Sheppard bolted back to the lab and was soon dragging McKay and Zelenka behind him. The waiting was over. The Wraith had arrived.

Sheppard, McKay and Zelenka were the last to enter the crowded briefing room.

"I thought we had another two days!" McKay complained when he arrived.

"They've accelerated," Chuck, the technician from the control room, explained. "At their current speed, they'll be here in a matter of hours."

Silence greeted this pronouncement. The tension in the air was almost palpable as those present let the realization sink into the assembly. They had been preparing for this for weeks, but that did not make it any less terrifying. The memory of the last Wraith attack was still fresh in everyone's minds.

"Alright," Elizabeth began, "where do we stand?"

McKay jumped in at once. "First, I've managed to reconfigure the shield's codes so that it will deflect drones as well as anything else that tries to kill us."

"That's good," Sheppard said, "But how do we fight back?"

"I was getting to that," McKay said impatiently. "I've been working on a way of flashing the shield."

Sheppard raised an eyebrow. "Flashing?" he asked incredulously.

McKay gave him a suffering look, but Zelenka answered the question. "Essentially, it means we turn the shield off long enough for a drone to pass through then reactivate it.

"Won't that leave the city vulnerable to attack?" Caldwall asked.

"Of course it would," McKay allowed. "That's why we only deactivate a small area for milliseconds at a time."

"But we have been having difficulties maintaining the shield's integrity while doing it," Zelenka added.

"Which I could have solved, given more time!" McKay finished.

Sheppard rolled his eyes, "You've had three weeks! Don't tell me that's all you've done!"

"No, as a matter of fact," McKay declared proudly. "I've also reprogrammed a number of drones to override the Ancient fail-safes."

"But, if we can't fire them through the shield," Caldwell observed, "then how does that help us?"

"Do I have to come up with everything?" McKay asked in annoyance. "You'll have to use puddle jumpers."

Sheppard frowned. "Jumpers don't carry enough fire power to take out a whole hive."

"I know," McKay admitted. "But if you can get close enough to knock out the power to the chair and weapons, we can lower the shield long enough to launch drones without worrying about a counterattack."

Sheppard winced. McKay made it sound so easy. "I'll do it," he consented. Sheppard was already running through his mind the list of other good jumper pilots who would also volunteer. It wasn't a mission he was going to order his men to do.

Elizabeth, who had been listening intently, nodded her approval. "Alright. What about repairs to the Daedalus?"

"We're on schedule," Caldwell informed them, "but I don't need to remind you that the Daedalus can not take on a full Hive in its current state."

"I know," Weir acknowledged. "What about the transporters?"

Caldwell shook his head. "Hermiod says it's impossible to get through the Wraith interference without more information on exactly what's causing it. If, however, Colonel Sheppard can knock out that interference along with their power, we should be able to transport objects in and out of the Hive."

"So, we can get Carson and Ronon out?" Rodney asked hopefully.

"If they are still alive," Caldwell replied. "We should be able to beam them out once the interference is gone."

Elizabeth and Sheppard exchanged an anxious look. The chance that either Ronon or Beckett was still alive shrank with each passing day. Though Weir still held out the hope they could be rescued, everyone knew it was a slim hope at best. Especially since Sheppard was sure that Carson's little act of saving their lives would not have made a good impression on his captors.

----------------

Carson nervously watched the Queen, trying to judge her mood. An hour ago he had injected George with the gene therapy he had managed to create. Now they were waiting to see if it had worked. Carson prayed that it would succeed on the first try. He didn't think the Queen would like an explanation of it not working in all subjects. More than that, he prayed that his tampering would not be discovered. If the Wraith had time to react it would be too late for his plan to do any good.

George ran his fingers over the life signs detector that Carson was sure had come from the team the Wraith had captured. It remained dark. Carson held his breath as the Queen's expression darkened. Then, the device beeped and the screen lit up, depicting several small dots.

"Excellent," the Queen smiled approvingly. "See that the drug is administered to all the Hive," she ordered.

"Yes, my Queen," George bowed. The lab became a flurry of activity as Wraith worked to prepare the injections.

The Queen stalked over to Carson, who had sagged with relief. "You have done well," she said with approval. "I am pleased."

"I don't suppose that means you'll let us go?" he asked.

The Queen's eyes danced in amusement at the suggestion. "Perhaps," she teased. "But first, you will witness the destruction of your people. I'm sure it will be a spectacular sight." She waved a hand and a pair of guards came forward to take him back to his cell.

Before they left, she leaned closer. "If you have deceived me, human," she growled. "You will wish I had fed on you long ago." With another wave, he was led away.

"What happened?" Ronon asked, when the guards had left. He was used to Carson's schedule by now and hadn't expected him for a few more hours.

Carson sat against the wall and closed his tired eyes. "The gene therapy worked."

Ronon leaned closer. "What about your plan?"

Carson shook his head. "No way to tell. It won't take effect for a few hours. If it works at all."

Ronon sighed. "So, we wait?"

"Aye," Carson confirmed. "We wait."

**-----------------**

John tapped impatiently on the jumper's controls and glanced outside. Vast, empty space, dotted with hundreds of stars met his eyes. He sighed. He wished he could have someone to talk to, but the mission was too dangerous for him to risk multiple personnel in a jumper. It had never occurred to him how empty the small space could feel without McKay, Teyla or Ronon in the other seats.

An insistent beep from the jumper's heads up display caught his attention. Sheppard hit the radio on his controls. "Lorne, Parker, come in."

"Go ahead, sir," the other two pilots chorused.

"The Wraith Hive just exited hyperspace," he announced, though their own jumpers would have told them that. "Maintain cloak and radio silence until ordered."

The two men confirmed and all three jumpers faded into black. Sheppard hoped three would be enough. Several more pilots had volunteered, but he had decided that surprise and stealth was the operative method. And so, he had gone with a smaller flight. It only took one to get through.

The huge, purple expanse of the Wraith Hive loomed into view. It hovered like a vulture over Atlantis as it released dozens of darts that dove for the surface. It hadn't fired any drones yet, but Sheppard wasn't going to wait until it did. He moved his jumper closer, zeroing in on the power signature shown on his display. Lorne and Parker fell in behind him as they neared their target. Sheppard glanced up at the display, trying to get an idea of how many darts he'd have to fight through to get clear.

He froze. Four dots were on the screen. Four puddle jumpers. He reached for his radio and as he did, another dot appeared. This was too much. He'd have to risk breaking radio silence.

"Lorne, Parker," he called. "You reading the signals on our six?"

"Yes, sir," Lorne confirmed. "I thought we were the only jumpers out here?"

Sheppard frowned. There should not be any other jumpers unless someone had disobeyed his orders. He got a sudden sinking feeling in his gut that something was very wrong.

"Major, go check out our new friends," Sheppard ordered. "Parker, stick with me."

"Yes, sir," Lorne replied. He eased his jumper back and turned it around so that it was facing the other signals, just as another joined them. Even though all he could see was blank space, his display confirmed the presences of three cloaked jumpers. He moved closer and tried to will his jumper to identify the strangers.

The jumper blinked a warning, and Lorne swerved out of the way, just as the other jumpers decloaked and fired. Yet instead of the Ancient drones, they were firing Wraith energy weapons. Lorne swore as another strange jumper moved to cut him off. He veered again, but the enemy bolts caught the jumper's side. The dark of space exploded into white. Then Lorne's vision faded to endless blackness.

"Lorne!" Sheppard's jumper did a complete 180 to find a very disturbing sight: Lorne's jumper was smoking and drifting aimlessly through space. Four other jumpers surrounded it, weapons armed. Now, Sheppard had no doubt who was at the helm of each one.

They were Wraith.

TBC…

AN: Sorry for the delay. I'll try to get the next few out faster. And so the excitement begins! Much action and whumping still to come! Great thanks to all who reviewed and left thoughts on the last chapter! It was very helpful and I really appreciate it!


	9. Chapter 9

Gene Warfare, by Rowana Farrin

**Chapter Nine**

Sheppard slammed on his radio control: "Daedalus! I need you to beam Major Lorne out now!"

Before he got a reply, the Major's puddle jumper erupted in a fireball of light. John's heart froze and he felt his breath catch in his throat.

"Daedalus?" he called desperately. He was hoping, praying, that they had been in time, but hardly dared to believe it.

"We have him," came Caldwell's short reply. John had never been so happy to here that voice.

"Colonel! What is going on up there?!" Weir asked urgently.

Sheppard didn't have time to answer her. Now that Lorne's jumper was gone, the Wraith jumpers were turning towards Parker and him. It was four on two. Not the best odds, but at least they had Ancient drones on their side. Nothing beat self-targeting missiles in a dogfight.

Sheppard dodged the first salvo of Wraith fire with Parker riding his tail. The Wraith followed a little less gracefully. Sheppard only hoped that the Wraith pilots stayed unfamiliar with the controls. The jumper, obeying Sheppard's mental command, had outlined the Wraith jumpers in red. At least he wouldn't end up hitting Parker when he fired.

Three drones shot from Sheppard's jumper and zoomed for the first pursuing Wraith. The Wraith attempted to dodge, but the drones followed the shaky movement and impacted the jumper's screen. Sheppard silently thanked McKay's genius as the enemy jumper exploded across the star scape.

The remaining Wraith were quick to retaliate and launched another barrage of fire. Sheppard swerved left while Parker dove downward. Two of the Wraith followed Sheppard, keeping up their attack as they came. John's mind worked furiously. Obeying his mental command, the jumper froze in space. The two following ships shot past and Sheppard let loose a swarm of drones that decimated another target.

A whoop of joy announced Parker's successful elimination of a third Wraith jumper. Sheppard silently congratulated the young pilot as he concentrated on tailing the last one.

"Sheppard! What the hell is going on up there?!" McKay's voice roared through his radio.

"The Wraith have puddle jumpers, McKay!" he snapped back angrily.

He was in no mood to explain the situation while he was busy trying to stay alive. Ignoring McKay's flustered response, Sheppard doggedly followed the last Wraith. A final volley of drones soon saw the end of the threat and Sheppard couldn't help grinning. So much for Ancient technology giving Wraith an edge.

"John!" Elizabeth called from the surface. "You need to get out of there, now! We're reading at least a dozen more jumpers coming from the Hive!"

"And we'll lose the city if I don't complete this mission!" he returned firmly. He turned his jumper back towards the Hive. He knew the risk he was taking, but at least it was his life on the line and not the lives of everyone else in Atlantis.

"Why are you always so suicidal?!" McKay shouted at him.

"Do you have any other brilliant plans for saving the our butts, McKay?!" John retorted angrily. Silence followed the remark and he knew he'd get no more protests.

"Parker," he called over his radio. "You'd better head back."

"With all do respect, sir," Parker replied. "You'll have a better chance with two."

Sheppard smiled and his respect for the man grew. He mentally made a note to recommend him for a promotion. If they survived. He glanced at the heads-up display, watching for the approaching jumpers. They weren't coming.

"What the...?" Sheppard exclaimed in confusion. "McKay! Where are those jumpers?!"

"What? They should be right...oh, no."

Sheppard's heart skipped a beat. That was never good coming from McKay. "McKay?" he began.

"They're not heading for you," Rodney replied. His voice was laced with a doomed finality. "They're heading for Atlantis."

"But the shield's up, right?" Sheppard asked desperately.

"It won't make any difference," Rodney replied, "the shield was designed to allow puddle jumpers to pass through it to defend the city."

"So, fix the shield!" John ordered. His cry was met with silence. "Rodney!" he shouted. "Elizabeth! Damn it! Somebody answer me!"

He turned his jumper around and sped towards Atlantis with Parker close behind. The jumper beeped a warning and Sheppard stopped short. A wall of Wraith drones flew between him and the city.

----------------------

Rodney clung to a control panel he as Atlantis shook with the first attack. His mind was racing through all the solutions that might save them. Every plan he could think of had one major flaw: time. It always took too much time. Time that was in despairingly short supply.

"McKay!" Elizabeth shouted from nearby. "How do we take down those jumpers?"

"It may not be possible!" he admitted. "If I had a little more time, I might come up with something..."

"We don't have time!" Weir reminded him. "We're sitting ducks!"

"A fact I am painfully aware of!" he snapped back.

The city rocked violently, making both of them grasp for support.

"What about our own jumpers?" she asked.

"I loaded all of our reprogrammed drones onto Sheppard's jumpers," he informed her sadly, cursing himself for not making more.

"They might at least buy us some time," Weir pointed out. She was already on her radio, calling for the jumpers to be launched.

"You'll be sending them out there to die!" McKay shouted in accusation.

"And we'll all die if we do nothing," Weir said firmly. She hated making these choices. "If they can keep the Wraith away from the shield generators..."

McKay snapped his fingers, cutting her off. His eyes lit up with a spark that broke through the despair.

"The shields..." he whispered.

"Rodney?" Weir questioned.

"I need technicians at one of the shield generators, now!" he ordered. He was already typing madly on his laptop. Outside, the tall spires of Atlantis were already on fire from the Wraith bombardment. They were running out of time.

"What are you planning, McKay?" Zelenka's voice sounded over the radio.

"Are you at one of the generators?" McKay barked, by way of answer.

"Yes, Rodney," Zelenka replied with immeasurable patience. "What do you want me to do?"

"Upload the fail-safe override into each of the shield generators!" he directed, clinging to the desk as the floor shook again.

"How does this help us?" Weir asked in a rush.

"The shield will blanket the city with the override signal," McKay explained quickly. "Then, we'll be able to use drones to take out the Wraith jumpers!"

"How long will this take?" Weir had to shout to be heard over the echoes of explosions from outside.

"It depends on how fast they can get the code installed," he replied, reluctantly admitting it was out of his hands. Then he turned and ran for the door.

"Where are you going?" Weir demanded.

"If this works, someone needs to be in the Chair room!" he explained tersely. He tore down the hallways, fighting to keep on his feet as the city quaked with each hit. He was terrified. So many things could go wrong, and one slip would doom the whole city. He cursed the intellect that made him the last hope for Atlantis and cursed the idiots around him that left it to him. If he failed, he had no one to blame but himself.

McKay reached the chair room just as Zelenka announced that they had finished adjusting the shields. McKay silently thanked his colleague; something he would never do out loud. He jumped into the chair and closed his eyes in concentration.

It was hard. Sheppard had always made it look so easy, but the drones fought his efforts to control them and went whizzing off in different directions. Desperately, he tried focusing on the Wraith-controlled puddle jumpers. Five drones flew where he directed and converged on one of the offending jumpers. It burst in a fireball of red and gold.

"It worked!" he heard Weir call gratefully over the radio. He smiled. How could she ever doubt his genius? Feeling more confident, he targeted the remaining jumpers, sending scores of drones zooming through the towers of Atlantis. One by one, the targets were destroyed.

"Well done, everyone," Weir was saying over the radio, but McKay barely heard her. He was focused on the last Wraith-controlled jumper. This one was being difficult. It was dodging around buildings so fast that it was impossible to keep a lock on it.

"Where are you going?" McKay muttered angrily. Before he could work it out, the Chair informed him. Blood drained from his face. He furiously ordered the drones to go faster, even though he knew they could not.

"Look out!" he screamed, but had forgotten to turn on his radio. His cry went unheeded. The rogue jumper slammed into the northwest corner of the city, decimating everything it hit. McKay's breath hitched. Atlantis shuddered and moaned. The shield flickered, held for a moment, then collapsed in a torrent of light.

McKay fought to keep his panic under control. It wasn't over yet, they still had a chance. "Zelenka?" he called, this time remembering to turn on the radio. "What's the status on the other generators?" If he could only reconfigure the shields to function with one less generator...

Getting no response, McKay tried again. "Zelenka!" Still nothing. Rodney was starting to get concerned. Were communications down as well? "Radek?" he asked, more quietly this time.

This time he got an answer, but not from the source he was expecting. "Rodney," Weir was saying softly. "Radek was at the destroyed generator. We've lost contact with him."

McKay froze, barely hearing the rush of voices now streaming through his radio. He couldn't imagine Atlantis without Zelenka. Though he would never admit it, the man was almost as smart as he was. And if he was dead, it was McKay's fault. He should have stopped the jumper. Should have warned them in time to escape.

Chuck's voice broke Rodney's stupor. "The Wraith Hive is bearing down on us," he informed the city. "They are preparing to fire."

TBC…

AN: Sorry it's a little short. Hope you liked the action! has been finicky of late, so I'm sorry if people have been unable to view my story or leave reviews. Thanks as always to my loyal reviewers! (and those that tried to!)


	10. Chapter 10

Gene Warfare, by Rowana Farrin

**Chapter Ten**

Floating above Atlantis and oblivious to the conflict ensuing around them, Carson and Ronon sat impatiently in their cell. It had been hours since they had last seen a Wraith and Ronon was beginning to wonder if they had been forgotten in the excitement. Grimly, he figured they would be remembered once someone got hungry. He only hoped he would get the chance to snap a few necks before they got their fill. He fully intended to leave his mark on the damn monsters before he died.

Of course, escape would be nice too, but neither he nor Beckett would be able to fly a Wraith dart and he didn't see any other way of getting off the ship. Still, if they could evade capture long enough to do some damage that would be worth it. All these thoughts were worth nothing without a way out of the cell. Ronon got up and paced again. Where were all the Wraith?

Carson gave a soft moan and rolled over on the floor. He had fallen asleep a short while ago, exhaustion finally winning over his fears. Ronon glanced at him, hoping his dreams were better than the nightmares he suspected the man was having. He sighed and leaned against the wall, cursing the creatures that had brought them into this. No man deserved what was likely coming for them, least of all the amiable doctor.

A movement in the hall outside caught Ronon's eye. He stiffened. Then he moved his head the barest inch so he could clearly see outside the door. It was a Wraith. Ronon was sure it was the white-haired one that Carson had dubbed George. His presence was not so surprising, but his appearance shocked Ronon.

The Wraith was leaning against one wall, heaving air into his lungs as if he could not get enough. He staggered forward, clearly making for the prisoners' cell. Ronon tensed, ready to pounce the enemy as soon as it came inside. He leaned down and gently shook Carson.

"What?!" Carson snapped awake with wide eyes.

"Shhh!" Ronon hissed. Not that it really mattered, the Wraith knew they were there. He nodded towards George. "What's up with him?"

Carson looked at the oncoming Wraith, who was now only a few yards from the cell. His eyes, once full of fear, grew sad.

"The gene degradation is taking effect," he said solemnly. "I didn't think it would be this fast."

Ronon gave him a confused look, but George staggered to the door before he could ask for further explanation. The Wraith looked paler, if that was possible, but his eyes blazed with fury.

"What have you done to me, human?!" he shrieked.

Ronon jumped up as George slammed the door control and staggered towards them. Fueled by rage and desperation, he lunged at Beckett with murder in his eyes. He never got that far. Ronon moved in swiftly and gave the Wraith's neck a might twist. The snap was deafening and George collapsed, lifeless to the floor.

Carson stared, first at George, then at Ronon, then back to George. He wasn't sure what shocked him more, that the Wraith had been so bent on killing him or that Ronon had killed him so easily.

Ronon's insistent voice broke him from his stupor, "We need to get moving."

Carson nodded dumbly and stood on shaky legs. They moved quickly out of the cell and down the maze of corridors. They had no particular destination in mind; they were moving on pure instinct and need to escape their captors. For a while, they encountered no Wraith, but it wasn't long before the clunk of footsteps warned of approaching enemies. Ronon shoved Carson into a small side room, following quickly behind him. Both men hardly dared to breath as they watched a pair of faceless drones pass by them without a glance.

Carson breathed a heavy sigh of relief. "I don' no how much more of this I can take," he whispered.

Ronon didn't answer, but inspected the hallway to be sure the Wraith had gone. Assured that the coast was clear, he turned back to find Carson staring at the far wall in horror.

"What?" Ronon asked in concern.

Carson just pointed. Ronon turned. What he saw made even his strong heart quaver. The window showed that the Hive was in orbit above a planet. A planet they both recognized in an instant.

"It's Atlantis," Carson whispered.

**----------------**

Sheppard swerved as a Wraith dart dove at him from above. Parker zeroed in on the offending ship and quickly dispatched it with a few drones. So far, they were holding their own, but Sheppard knew they would not last much longer. The Wraith outnumbered them almost twenty-five to one. They had only lasted this long because the shear number of Wraith darts made it difficult for them to attack without interfering with each other.

Sheppard fired off another two drones at a dart that was trying to tail Parker. He wasn't sure how many drones a puddle jumper held, but he was sure he must be running low by now. At least while the darts were firing on them, they weren't attacking Atlantis.

The proximity alarm on the jumper beeped a warning. Sheppard spared it a brief glance and felt his heart sink. The Hive ship was on the move and heading for the planet.

"Atlantis, this is Sheppard," he called urgently, dodging another dart as he did so.

"Go ahead, Colonel," Weir replied. Her voice was tense and worn.

"The Hive ship is heading in your direction," he warned her, trying to keep his voice cool. After all, Atlantis still had the shield to defend itself.

"We're aware of that," Weir informed him. "But the last attack took out our shield."

"What?!" Sheppard practically screamed. Momentarily distracted, a dart made a pass to his left, scoring several hits. John cursed and dispatched the dart before shouting back. "So, get it back on!"

"There isn't enough time!" Weir shouted back. Her voice betrayed her rising fear. "You need to get back here, we're evacuating the city!"

"Damn it!" Sheppard cursed. He knew he had no way of getting back without leading the swarm of darts to the city. "Don't wait for us!"

John didn't hear the reply as a large explosion burst across his view. He squinted as the light dimmed. He was sure he hadn't fired a shot.

"Parker?" he questioned. "Was that you?"

"Negative, sir," the young man replied, equally confused.

Sheppard was just about to bring up a scan of the debris when a dart swerved in front of him. He swore and readied another drone, but stopped when the dart moved again out of his vision. He raised an eyebrow; the Wraith was flying as if it were drunk. Curious, he turned the jumper to follow its progress, glancing at his display to keep an eye on the rest of the darts.

All the darts were swerving uncontrollably. Two of them veered too close to each other and exploded in a burst of fire. Several others just floated lifelessly in space, becoming obstacles for the rest of them. More collisions soon followed, severely depleting the number of darts in space.

"Atlantis?" he called in disbelief. "Are you seeing this?"

"We see it," Weir confirmed. "What's causing it?"

"I don't know," Sheppard admitted. "It's almost like they're sick or something."

As he said it, John couldn't help but wonder if Beckett had something to do with it. He wouldn't put it past the doctor to poison a Hive full of Wraith. He just hoped that whatever it was wasn't affecting Carson and Ronon too. Or worse, getting them killed.

---------------

Ronon tore his gaze from the sight of his new home and looked back at Carson. "So what did you do to the Wraith?" he asked.

"What?" Carson was still distracted by the thought that he had led the Hive to Atlantis. He turned to Ronon with a frown. "I'm not sure how ta explain it."

"Try," Ronon insisted.

Carson nodded and took a deep breath. "The Wraith don't have many of the inhibition proteins we humans have that result in aging. I introduced an active retrovirus inta the gene therapy to simulate those proteins. It slowly degrades the subject's chromosomes by eatin' away at the telomeres until it gets to the vital genes."

Ronon just looked at him and Carson sighed.

"Basically, the virus is slowly removing the genes they need to survive. Eventually, the degradation will progress to a point that the cells can no longer sustain life. They start to decay at an accelerated rate."

"So, it'll kill them, right?" Ronon asked.

"Aye," Carson admitted, sadly. "If I had had more time I coulda made it less lethal..." he said regretfully.

Ronon snorted dissmissively. He liked it fine if it killed. He saw no reason to be merciful to any Wraith, much less these ones. Speaking of Wraith, he hadn't seen one in a while. He glanced out into the hallway again, but found it eerily silent. Well, hanging around here was getting them nowhere, he decided.

"Come on," he told Beckett, before marching out into the passage.

"Where are we going?" Carson asked, hurrying to follow him.

Ronon shrugged and kept moving. They saw few Wraith on their journey and those they did find were too busy collapsing in agony to pay attention to them. It seem Beckett's retrovirus was extremely effective.

Carson felt his stomach grow more nauseous with each dying Wraith they passed. Much as he disliked them, he could hardly fear them now as they lay gasping for life. He felt horrible. As a doctor, he wasn't supposed to do harm to anyone, even life-sucking aliens. He had dared to hope that his virus would only incapacitate them enough to escape, not kill them all. He now realized it had been a vain hope.

Their path took them in front of a set of large, open double doors. Inside were strange control panels that seemed to grow from the flow like odd toadstools. A large window displayed the planet growing ever closer. The Wraith here were already dead, leaving Ronon and Carson alone.

Carson walked over to one of the panels. "Think we can fly it?" he asked.

Instead of answering, Ronon let out a roar of fury that caused Carson to whirl around in shock. The Wraith Queen, hair wild and eyes deadly, had leapt front the shadows and was heading straight for him. Carson stood frozen, too terrified to move. Then Ronon barreled into her from the side, knocking her to the floor.

The Queen hissed in fury and rose gracefully. "You will pay for what you have done, humans!" she shrieked. "I will enjoy your suffering as you die!"

She charged at Ronon, who grabbed her wrist and forced her hand away from his chest. She glared at him and slammed her left hand into his side. Breathily winded, Ronon stumbled but maintained his hold. Fueled by weeks of pent up energy and rage, he threw himself forward. Both combatants toppled in a heap on the floor.

The Queen narrowed her golden eyes. Ronon was suddenly fighting desperately for control of his own mind as she invaded his head. Distracted, Ronon was unable to stop himself from been flung forcefully by the Queen's next attack. He flew across the room and struck heavily against a wall.

"Ronon!"

Carson rushed forward to help and unconsciously placed himself between the Queen and his friend. She lunged and grabbed him viciously around the neck. Caught from behind, Carson struggled vainly against her vice-like grip as he felt his breath being choked away for the second time.

The Queen leaned close and hissed in his ear. "Do not think I will give you such an easy death!"

Before Carson could comprehend the significance of the statement, he felt her grip weaken. Sweet air had rarely tasted so good as Carson dropped to his knees gasping. After several seconds, he looked up and almost choked again. The Queen lay sprawled next to him, her sightless eyes still glaring. A long knife was sticking from her throat.

He turned to look at Ronon, who was sitting where he had fallen. His left arm hung limply, but his right was still outstretched towards the Queen.

"Where did ya get that?!" Carson asked breathlessly.

Ronon just looked at him and shrugged.

Carson shook his head and tried not to think of the places the man could have been hiding it. "I'm just glad you didnae miss!" he exclaimed.

"I don't miss," Ronon said firmly.

Carson nodded gratefully and moved towards him. "Let me look at ya, then."

Ronon hissed as Carson ran his hands over his arm.

Carson frowned. "It's broken."

"I noticed," Ronon said grumpily.

"If only I had something to splint it with..." Carson looked around the room hopefully. "Oh, dear."

"What?" Ronon asked, struggling to stand.

Carson pointed at the window where the blue planet nearly dominated the view. "Is it just me or are we getting closer?"

Ronon frowned. Carson was right, they were getting closer. Not only that, but he was sure they were getting faster too.

TBC…

_AN: I finished early! You lucky people! So I figured I would post it early too, since you all have been so patient with me. Next chapter should be up on time this weekend as well. The genetic stuff should be fairly accurate, since I based it off stuff I learned in class. Whether or not it's possible in real life I have no idea. And don't worry, I haven't forgotten poor Zelenka. ;) Many thanks as always! _


	11. Chapter 11

Gene Warfare, by Rowana Farrin

**Chapter Eleven**

Sheppard allowed himself to relax a little. Only a dozen or so Wraith darts remained, drifting harmlessly through space. It finally looked as though they might actually get through this. He glanced up at the floating Hive ship. It had been silent for several minutes, despite the fact that Atlantis lay defenseless below it. Yet, it was still moving.

"Atlantis, this is Sheppard," he called.

"We're still here, John." Elizabeth's relief was audible, even over the radio.

"That's good to hear," Sheppard replied amiably. "But you do realize you still have a Hive ship heading straight for you?"

An uncomfortable silence followed the remark.

"This is not good," McKay's pessimistic tones broke the quiet.

"McKay?" Sheppard tried to keep his voice calm, but he was a little too tense.

"The Hive ship isn't decelerating!" McKay explained in a rush. "At its current trajectory it'll crash less than a mile from the city!"

Sheppard winced. That was close. "So, what's the problem?" he asked.

"The problem?!" Rodney's voice rose incredulously. "The problem is that the impact will create a tidal wave twice as big as any we've previously seen! And without a shield, the city will sink and we'll all drown! That is if we aren't crushed to death first!"

"So, fix the damn shield!" John snapped angrily. He tried to push the puddle jumper's engines to go faster, but he knew that even if he could reach the Hive, he wouldn't be able to stop it. There was nothing he could do. And he hated it.

------------

McKay tried to think through the panic in his brain. Certain doom twice in one day was not good for his infernal pessimism. How was he supposed to fix a destroyed shield generator in a matter of minutes? He stopped rambling as a thought came to him. Not fix the generator, replace it! That might work! If only he had enough time.

"Hermiod!" he shouted over the radio. "I need to be in the engine room!"

A flash of white light and he was faced with the impassive Asgard. "What are you planning, Dr. McKay?" he asked calmly.

"I need to borrow the Daedalus's shield generator crystals," he said urgently.

Hermiod's large black eyes narrowed. "Many of the crystals are undergoing repair," he reminded, "and they may not be compatible with Ancient technology."

"We don't have time for debate," McKay barked. "Beam me and the crystals to the damaged generator, now!"

Hermiod made a few irritated remarks in the Asguard language. A second later, McKay was standing in the remains of the northwest generator station. It was in ruins. Most of the ceiling had collapsed into piles of rubble that blocked the corridors. Only the dim glow of emergency lights and McKay's small flashlight lit the small space remaining to stand in. The generator itself was in shambles and emitting occasional annoyed sparks into the gloom.

"Oh, boy," Rodney muttered.

This was worse than he had thought. Even with replacements from the Daedalus, he wasn't sure if he could fix it, much less on a time limit. He stuck the flashlight in his teeth and heaved away some of the debris.

"Rodney?" Elizabeth called urgently, "what are you doing?"

He had to take the flashlight out of his mouth to respond. "I'm trying to interface the Daedalus's shield generator crystals with the city's," he informed her. "If it works, we should be able to get the shield working at least long enough to avoid total destruction."

"Can we help?" she asked.

"You can stop bothering me with annoying questions and let me get to work!" he replied, a little more forcefully than he'd meant.

He yanked a panel off the wall and gazed inside at the shattered crystals. "Oh, boy," he muttered again. This was going to take a lot of work.

------------

The Hive careened through the atmosphere, gathering momentum as it went. Fire and heat seared its side until it looked more like a fireball than a ship. Parts of it were breaking off and flying away under the stress and friction. Only the shear size of the vessel allowed most of it to remain intact through the descent.

"We're gonna crash!" Carson cried, clinging to the Wraith controls.

"So, stop it!" Ronon demanded. He was fighting to stay upright as the ship shook itself apart around them.

"What do ya expect me ta do!" Carson's accent was getting thicker with his terror. "I don' know the firs' thing about space ships!"

"Slow us down!" Ronon barked angrily. They did not have time to panic.

"I can't!" Carson wished he paid more attention to McKay's rambling explanations. Then, maybe, he might have at least thought of something useful. Not that Rodney had ever been stuck in a Hive ship making a nose dive for a planet.

The ocean was rushing towards them at a frightening speed. _At least we missed Atlantis_, Carson's frantic mind thought. Then, his was thrown forward by the violent impact and knew no more.

---------------

Elizabeth ran out onto the balcony in time to see a massive trail of flames erupt in the ocean not far away. The site was breathtaking and, under any other circumstances, amazing. If it hadn't been so close. And so deadly.

"McKay!" she shouted over the radio.

"I'm working!" he screamed back.

Elizabeth watched in awe and fear as a wall of water rose in front of her. The moment seemed to be holding its breath as the terrifying force of nature rose above her. It towered over the city like a waterfall in space, poised to unleash its power.

"Rodney," she breathed, hardly daring to hope.

"I got it!" came the triumphant cry.

A wall of light rose to meet the water and the two collided in a crash of sound. Water coursed down the invisible dome in streams. The rising sun pierced through the rivulets of water, bathing the city in a crystal light. Elizabeth was sure she had never seen anything so beautiful.

-----------------

McKay sighed with relief. They really needed to stop cutting it so close or he was going to snap under the stress. He leaned carefully against a reasonably undamaged wall. He really needed to ask for a day off.

A sound echoed alarmingly in the stillness. McKay jumped and swung his flashlight around. This part of the city should be empty. His already strained mind raced through all the possible answers: loose debris, ventilation problem, Wraith. His breath caught. What if a Wraith had gotten into the city? He grabbed frantically at his side arm and starting pointing it in every direction.

"This is McKay!" he whispered desperately, "I think I have a problem here!"

He missed the answer as another sound made him jump and whirl around. His flashlight fell on a pile of rubble. The sound repeated itself, and this time. Rodney was sure it sounded like a cough.

"Hello?" he called tentatively.

Something shifted, dust scattered, and a small cry reached McKay's ears. He started and bent down on the floor, pointing the beam of light into the small crack between the floor and the recently dislodged ceiling. The light caught something that reflected it back, along with a string of familiar curses.

Rodney screamed and dropped both his flashlight and his gun. Taking a deep breath, he squinted through the dim light. "Radek?"

The figure coughed again, but managed to mumble a few more words in Czech that Rodney didn't recognize.

McKay sighed in relief. "Oh, thank god. I thought you were..." he stopped when Radek coughed again, harder than ever. "You ok?"

More curses followed this question. Rodney winced at how bad his friend sounded. "Alright, stupid question," he admitted. Worry was starting to creep back into his mind. So far, Zelenka had yet to say anything in English and McKay was sure that being crushed under half of Atlantis could not be good for the man. He needed help, fast.

"Hang in there." He tapped his radio. "This is McKay."

"Rodney?" Elizabeth asked in concern. "What's going on down there?"

"I've found Radek," he answered urgently. "He needs help, now!"

"I can have the Daedalus beam a medical team to you," Weir suggested.

McKay shook his head, before he remembered that she couldn't see him. "There's barely enough room to breath in here. Have Hermiod beam us directly to the infirmary."

"Understood."

Seconds later, McKay was pushed aside as medical personnel rushed to treat Zelenka. Rodney caught a glance of him before his was wheeled away. He looked terrible, worse than Rodney had envisioned. He was covered in dirt, sweat, and blood. His glasses were cracked and askew on his nose. The blood seemed to mostly be coming from a slash in his right arm. McKay caught a few lines from the nurses about "concussion" and "internal bleeding", but they were gone before he could demand more information.

Rodney suddenly felt exhausted. He sat down heavily on a nearby chair, just as Dr. Weir and Sheppard came running into the room.

"How is he?" Elizabeth asked kindly, noting how tired and dejected he looked.

Rodney shook his head. "I don't know," he confessed sadly. "He looked horrible. I don't think he even recognized me."

"He'll pull through," John assured him confidently.

"He'd have a better chance if Carson were still here," Rodney said quietly. "We've got to find him!" He stood up quickly. "If they were still alive, there's a chance they could have survived the crash!"

Weir's eyes lit with sudden hope, then she frowned. "But that means the Wraith could have survived as well."

"All the more reason to leave now!" Sheppard insisted.

Seeing the determined looks on both of their faces, Elizabeth relented easily. In truth, she had already decided to let them go, but she had felt the need to point out the risk. "Alright. Can the Daedalus transport a team inside?"

"No," Rodney said regretfully. "Whatever was blocking their signal is still active. We need to get inside and disable it before we can beam anyone in or out."

"How?" Weir asked.

"We'll use a jumper," Sheppard stated. "Go in, find Ronon and Carson, and get back out."

Weir nodded. "Take who you need. And good luck!" They were out the door before she could finish.

-------------

"Did I mention how much I hate these things underwater?" McKay asked nervously.

"Many times," Teyla assured him patiently.

"We're almost there," Sheppard added.

The three of them, plus five well armed marines were on their way to the sunken Hive. At this depth, the water was inky black and the signal light affixed to the puddle jumper only illuminated a small area.

McKay peered into the blackness. "We should be close enough to...Woah!"

The purple mass of the Hive practically jumped into their vision. Even dead and crushed under several hundred feet of water, it was an unnerving sight.

Sheppard brought up the heads-up display. "We'll head for the dart bay."

"What if it is flooded?" Teyla asked.

"We should be able to find some kind of airlock," McKay said with little confidence. Sheppard eyed him critically and he sighed. "Alright, I _think_ we could find an airlock. We don't exactly have many options here."

"Alright," Sheppard said jovially. "Let's find an airlock."

As it turned out, the Dart bay shield was thin, but still intact and keeping the water at bay. Sheppard landed the jumper on one of the empty docks and they all disembarked.

"Three of you stay with the jumper," he ordered the Major. "The rest, with me."

The commanding marine nodded and sent two of his men with Sheppard's team, while he remained. They moved slowly into the interior of the ship, Sheppard eyeing his life-signs detector as they went.

"Teyla, are you sensing any Wraith?" he asked suddenly.

"No," she replied. "Nothing."

"I'm not getting any life signs, either."

"What does that mean?" McKay asked anxiously.

Sheppard cut him off with a hand as he spotted a shape in one corner.

"Stay here," he ordered the marines.

"What is it?" McKay asked as he, Teyla, and Sheppard moved to investigate.

Sheppard glared at him to be quiet as the glow of their flashlights lit the slumped figure. It was a Wraith. Sheppard poked it tentatively with his gun.

"It's dead," he said with surprise.

"What?" McKay was just as shocked, "How?"

"I'd sure like to know," Sheppard confessed.

The Hive ship rocked suddenly and a door behind them slid shut with a snap. They ran back to find themselves separated from the two marines.

"McKay!" Sheppard snapped.

McKay already had his laptop hooked into the door panel and was typing madly. "It's no good," he admitted. "The ship is sealing parts of itself to prevent flooding."

"Does that mean that this hallway is filling with water?" Teyla asked urgently.

"Yes," he answered.

"So, get the door open!" Sheppard ordered. "Thompson and Rilley are in there!"

"I can't!" McKay snapped angrily. "Even if I could override the security protocols, the compartment is filling too fast to get them out in time!"

"Try!" Sheppard demanded.

"It's already too late!" McKay insisted, but turned back to his laptop.

Sheppard glared at him in fury and glanced down at his life-signs detector. Five dots registered on the screen. He watched pensively as McKay continued to work. Minutes later, two dots had winked out. Thompson and Rilley were dead and the puddle jumper was on the other side of the blocked door. Sheppard and his team were trapped on the rapidly flooding Hive ship.

TBC…

_AN: I wouldn't make it _that_ easy! ;) Thanks to everyone who's been sticking with me! I finally figured out how private messages and such work, so I'll be giving my reviewers some happy replies as thanks. Sorry that I forgot about Teyla for so long. I have a hard time writing her so she sometimes gets ignored._


	12. Chapter 12

_AN: I am so sorry for the huge delay! Real life has been evil. This chapter is nice and long to make up for it!_

Gene Warefare, by Rowana Farrin

**Chapter Twelve**

Carson groaned and blinked his eyes open. His passing hope that he would wake up in his own infirmary was dashed when he saw the familiar expanse of Wraith architecture. He moaned and rubbed his sore head before striving to sit up. After a few seconds of wooziness, his brain settled and he was able to focus on his surroundings.

"Ronon?" he called softly.

A shuffling noise echoed from across the room. "Still here," Ronon grunted.

Carson struggled stiffly to his feet. He felt several painful bruises in various parts of his body, but nothing more serious. He supposed he should feel lucky, yet he couldn't ignore the fact that they were still trapped. Escape was just as impossible as it had been a few hours ago.

He moved over to where Ronon had settled against a wall. "How's the arm?"

"It's fine," Ronon insisted.

Carson raised his eyebrows. "That's a likely tale. Let me see." Reluctantly, Ronon allowed Carson to check over his wound. "Well, it doesn't seem worse, but I'd still like ta get a splint. Any other injuries?"

"No," Ronon replied, wincing at the doctor's ministrations. "What about you?"

"I'm fine," Carson answered simply.

Ronon narrowed his eyes suspiciously. "You were out for a while."

Carson sighed and rubbed his temple. "How long?"

Ronon started to shrug, but stopped himself quickly when his arm protested. "Maybe an hour."

Carson logged the information away to worry about later. He had other things to be concerned about right then, like imminent death by either suffocation, dehydration, starvation or some combination of the three. "Let's get to work on that arm of yours," he said.

After much grumbling from both men and the use of the Queen's dress for bandages, Carson strapped Ronon's arm to the Setedan torso. He wished he had a real splint available, but did the best with what he had. Ronon spoke little and only gritted his teeth against the pain.

"I won't be much good against Wraith like this," Ronon complained.

"I think Wraith are the least of our concerns," Carson admitted. It was not a pleasant thought. He looked around gloomily and tried to ignore the drums in his head. "We need to get out of here."

**---------------**

"Are you sure we're not going in circles?" Sheppard asked impatiently.

"Yes, I'm sure!" Rodney snapped back. He waved ahead. "We're heading for the bridge so I can turn off the the signal that's interfering with our transporters."

"Just checking," Sheppard replied defensively. "Find anything, Teyla?"

Teyla stood from examining yet another Wraith corpse. "Nothing. They are all the same. It is as if they all collapsed from some illness."

McKay frowned. "Do Wraith do that?"

"I have never heard of such a thing," she confessed.

"At least for once it's a good thing," Sheppard put in cheerfully. "I hate it when we get those unpleasant surprises." He glanced down at the life signs detector and tensed. "I've got two life signs ahead," he whispered urgently.

"Wraith?" McKay asked nervously.

"I do not sense any Wraith," Teyla reminded him.

"Oh," Rodney perked up considerably. "It could be Beckett and Ronon!"

"Let's not jump to any conclusions," Sheppard told them. As much as he wanted to think it was their friends, it almost seemed too much to hope for. Besides, they knew that the Wraith kept human slaves and the life signs could easily be some other captives. He moved forward down the hall to find his way blocked by a large door.

"Can you open this?" he asked Mckay.

"Give me a second," he answered automatically, tapping at his tablet.

Exactly twelve seconds, later the doors slid open with a whoosh. Sheppard jerked his P90 up just as a hand shot out and put a knife to his throat. For a tense moment no one moved.

"Sheppard?" a surprised Ronon croaked.

"Ronon?" an equally shocked Sheppard answered.

"Oh thank God," Rodney and Carson breathed at the same time.

John resisted the urge to hug the pair of them. This was definitely the best thing to happen to him all day, included having the Wraith miraculously drop dead before wiping out all of Atlantis. They were both a mess; covered in bruises and the stink that comes from not having showered in several weeks. Ronon's left arm was in a makeshift sling and Carson's eyes looked glazed and bloodshot, but they were otherwise in one piece.

McKay was his normal eloquent self. "You look terrible!" he declared.

"Aye, Rodney," Carson confirmed wearily. He grinned. "And I have never been so glad ta see you."

"It is good to see you both alive," Teyla smiled. "But we should find a way to get off this ship."

Rodney raised a finger in triumph. "Way ahead of you." He waved a hand around the dimly lit control room. "Once I turn off the blocking signal, the Daedalus will be able to transport all of us back to Atlantis."

"And where exactly would this signal be coming from?" Sheppard asked reasonably.

Everyone looked around the large room full of unknown controls.

"No idea," McKay admitted.

"Great!" Sheppard glanced around the room again and reached for his pocket. "Then, let's make it easy."

"What?!" McKay recoiled. "You can't just blow everything up!"

"Yes I can."

"May I remind you that this ship is highly unstable? If you just go blowing holes in it, the whole thing could collapse on our heads!"

"Do you have a better idea?"

"Sounds like a good idea to me," Ronon submitted.

"It's an insane idea!" Rodney insisted.

"Do I get a say in this?" Carson asked politely.

Sheppard was still pulling C4 out of his pockets. "Nope."

Teyla eyed the explosives warily. "I think it would be wise to move outside."

She grabbed a protesting McKay by the sleeve and dragged him out into the hallway with Ronon and Carson close behind. While Sheppard busied himself laying charges, McKay began describing all the different ways this plan could get them killed.

"...and the structural integrity of the hull could be compromised," he was babbling, "causing several hundred tons of water to come crashing down on our heads!"

"McKay!" Sheppard snapped in annoyance as he came through the door. "I thought you said that was going to happen anyway!"

"Yes, but this way it will happen even faster!" he insisted.

John glared at him and shepherded them all further down the hall. He couldn't ignore McKay's warnings, but they didn't have time to wait. The water pressure was increasing all the time and soon it wouldn't matter whether they blew up the hull, the water would do it for them.

"Get ready!" he ordered.

After a quick look to see them all huddling for cover, he pressed the button. The silence that followed lasted for a full two seconds before it exploded in a rush of noise. Sheppard caught a glimpse of the devastation rushing to meet them and wished, for once, that McKay had been wrong.

------------

Carson woke with a splitting headache for the second time in the same day and his first thought was that the universe seemed to be out to get him. Then he heard McKay's whining voice and he knew it was.

"I'm telling you," he was saying, "I could be seriously injured here!"

"It's just your hand, McKay!" Ronon barked at him. "Shut up!"

Carson sighed and tried to sit upright, but had his body was not complying well. He felt a hand on his shoulder and looked back to see Teyla's face, barely visible in the light from the flashlights.

"Are you alright?" she asked kindly.

"Carson? Are you awake?" McKay inquired from nearby. "Can you look at my hand?"

"McKay," Ronon growled a warning.

Carson tried to clear his mind of the haze and attempted to focus on the situation at hand. He had heard Teyla, Rodney, and Ronon's voices and that left only one missing. "Where's Colonel Sheppard?"

The pause that followed was not reassuring.

"I think he's behind you somewhere," Rodney said quietly, dropping his own complaints for once.

Teyla moved the flashlight. Carson turned and his heart sank as he spotted a messy head of hair, matted with dirt and blood. John looked worse than Carson felt, which was saying a lot. _No rest of the weary_, he thought. He took a deep breath and called upon his last remaining strength. It was time to get to work.

Colonel Sheppard's legs were half hidden by the remains of the ceiling. It was impossible to tell how badly he was injured, but the spreading pool of red under his head was not comforting.

"Here," Carson passed the flashlight to McKay, "hold the torch up."

"How can I hold anything with a broken wrist?!" Rodney asked incredulously.

"Ya have two hands don'cha?" Carson had no patience for once.

McKay grumpily took the flashlight with his left hand and held it so that it illuminated Sheppard.

"Lift him up a little, lass," Carson instructed Teyla.

As she gently moved John's head into her lap, Carson fought past the haze in his mind and concentrated on remembering his years of medical experience. It seemed much harder than it should have been. Sheppard's skull was bleeding slowly, but appeared superficial. It was difficult to see his legs, but judging from the odd angle of one knee, Carson could surmise that something was broken. What was of real concern was the possibility of some kind of spinal injury. It was impossible to be sure under the circumstances and they couldn't risk moving him and doing more damage. Yet the eery creaking of the water pressure outside emphasized that they couldn't risk staying here either.

The others remained silent while he worked. Ronon was watching moodily, itching to finally escape the Hive ship. McKay was running through all the different ways they could escape in his mind. Unfortunately, nearly all of them ended with them dead.

Carson was trying to think of a way to free Sheppard's legs without doing more damage when the most wonderful sound broke the gloomy silence.

"Can anyone hear me? This is Dr. Weir. Please respond."

Carson was sure he'd never heard anything more beautiful in his life.

McKay fumbled for his radio, dropping the flashlight in the process. "Elizabeth! Please tell me you've got the transporters working?"

"Yes," Caldwell confirmed. "The other half of your team returned with the jumper an hour ago. But we weren't able to get a signal through until now. What's your situation?"

Carson grabbed the radio from Rodney. "Colonel, you need to transport us all ta the infirmary and have surgery teams prepped right away!"

"Carson?!" Elizabeth gasped. "Thank God! Is Ronon with you?"

"Aye, lass. And we could all do with a rest."

"Hang on. We'll have you back home in no time."

"That's good to hear."

Seconds later, the dismal blue walls of the Hive faded away to be replaced by shining Ancient architecture. Almost before Carson could recover from the sudden change of scenery, he was pounced by a dozen medical personnel who had never looked so happy to see injured people in their lives.

Feeling more like himself than he had in weeks, Carson immediately started drilling his assistants on everyones' condition and giving out instructions. Within minutes, Sheppard was whisked away for stitches and X-rays, and once McKay, Teyla, and Ronon were assured that he would be fine, they concented to be examined as well. Carson had just settled down to let himself get checked out, when he caught part of McKay's anxious conversation.

"Well how is he?! It's a simple enough question!"

"What are ya talking about, Rodney?" he asked tiredly.

"Radek." Carson caught the hint of concern in his friend's voice. "He was in surgery when we left."

"Ack!" Carson jumped off the bed and moved to find his new patient, followed by McKay and a pair of irritated nurses. They almost ran into Elizabeth when they rounded the corner.

"Shouldn't you be in bed?" she asked in concern. "You look terrible!"

Carson waved a hand. "In a minute."

Zelenka was in the intensive care unit, surrounded by whirring and beeping machinery. He looked better now that he was cleaned up, but he was too still to be healthy. The nurse on duty stood in surprise when he saw them.

"Dr. Beckett. Shouldn't you be resting?"

Carson waved him aside and grabbed the chart at the end of the bed. A quick look told him that Zelenka had a few fractures and lacerations that had all been tended. The real issue was that he had lapsed into a coma and the cause had yet to be determined. Carson wracked his brain.

"Rodney, was he talking when you found him?" he asked.

"What?" Rodney jumped. "I don't know. Maybe. He was mumbling in Czech or something."

Carson bit his lip and reached for one of the Ancient scanning devices. A quick run over Radek's skull confirmed his fears.

"He had an inter cranial hemorrhage," he told them. "A small one thankfully, but we need to release the pressure now before it causes permanent damage."

He managed to get out a few orders to the nurse to prepare for surgery before the first wave of dizziness hit. He grabbed the edge of Radek's bed for support and tried to fight past the nausea. _Not now_, he begged, _I'm not done yet_.

"Carson?" Elizabeth laid a comforting hand on his shoulder. "Are you alright?"

"Mmm' fine," he mumbled.

"Maybe you should lie down and let someone else look at you," she encouraged softly.

"No," he insisted, pushing away from the bed. "I've still got things...ta..."

He never finished. The threatening darkness finally won the battle for control. Carson didn't even feel Elizabeth and Rodney catching him before he fell.

TBC….

_AN: Sorry again! I have been sick and unable to write for the past few weeks, but am doing much better now. The last chapter should be up soon! Thank you so much for your patience and encouragement! Special thanks to Malka for help with the medical stuff but remember that neither of us are doctors so forgive us for mistakes in jargon._


	13. Chapter 13

_AN: Once again, sorry for the long delay! I hope you enjoy the conclusion!_

Gene Warfare, by Rowana Farrin

**Chapter Thirteen**

"I'm telling you, that can _not_ be sanitary!"

"Why don't you tell him that and let the rest of us get back to sleep?"

"Are you crazy?! That monster will rip my arm off!"

The familiar voices stirred Carson from his sleep. At first, he wondered if it was still a dream because he knew the owners of those voices weren't with him on the Hive ship. Then his mind pieced itself together and he remembered. The Wraith were dead. He was back in Atlantis. He was safe. They were all safe.

His left arm tingled uncomfortably and he was suddenly aware of a sharp pressure clinging to him. He tried to pull away, but the force came with him. Had they restrained him? Why?

"See!" cried McKay from somewhere nearby. "It's probably cutting off circulation!"

The 'it' in question writhed and hissed on Carson's arm. McKay shrieked and Carson finally got the energy to open his eyes, just in time to see Rodney jump away, clutching his left hand as best he could with his bandaged right one.

"It bit me!" he cried. "Did you see that! It bit me!"

"Shut up, McKay!" growled Sheppard from somewhere nearby. "You'll wake Carson up."

"Too late for that," Carson mumbled, just loud enough for them all to hear.

Everyone turned to look at him. John was in the bed next to his with his leg in a cast and a bandaged on his head. Radek was on his other side, still asleep. How he could sleep through the noise, Carson didn't know, but he made a mental note to ask his secret sometime. Rodney was standing next to Carson's bed looking indignant.

John grinned. "Good morning, Carson!" he said cheerfully.

"It's afternoon," Rodney pointed out grumpily.

"What happened to yer hand?" Carson asked.

Rodney scowled. "Ask your beast!"

Carson glanced down at his arm to see Jamie curled so tightly around it that the creature looked like a scaly armband. Jamie made a high trill noise of pleasure and rubbed his nose against Carson's hand.

"He hasn't let go since you came back," Cadman said, entering the room. She smiled. "It's good to see you awake."

Carson smiled back. "It's good to be awake."

-----------------

Ronon circled his enemy searching for any sign of weakness. There! An opening! He lunged forward only to be sent sprawling as a stick struck him across his uninjured shoulder.

"Are you sure you should be doing this?" Teyla asked.

"I'm fine," he grunted.

Teyla raised an eyebrow and looked at his broken arm.

Ronon scowled. "I'm just out of practice," he insisted.

"Are you sure there is nothing is troubling you?"

"Yup."

She shrugged. "You were a prisoner of the Wraith. I imagine it was not a pleasant experience."

"I don't want to talk about it," he declared, lunging at her.

Teyla easily sent him sprawling again. "Are you sure?"

He grunted and accepted her offered hand. "I think maybe I should get my arm checked," he said, turning to leave.

"You could not have done anything different," she told him.

He paused. "I should have been able to prevent it. It's my job to protect all of you."

"And you did," she insisted. "Were it not for you, Carson would be dead."

"And if it weren't for me," he said without turning around, "he wouldn't have had to work for the Wraith."

He tried to leave again, but Teyla's next words stopped him. "Do you really think he would have survived if he had not had someone to protect?"

Ronon wasn't sure what to say to that. Especially since it was true.

----------------

For the next few days, it seemed that everyone in the city found some excuse or other to visit the infirmary and see Dr. Beckett. Though he was flattered by all the attention, Carson was soon wishing for peace and privacy so he could think. The events of the last month were not easy to forget and nightmares still plagued even his waking mind.

Finally, he was able to convince his staff to let him out of their sights for a few hours. After a long walk around the city, during which everyone he passed stopped to say hello, he found himself on the balcony behind the control room. The sight of the vast ocean and endless sky was calming. He leaned on the railing and watched the waves while absently rubbing Jamie's head. The lizard still hadn't let go of his arm.

"It's nice, isn't it?"

He turned to find Elizabeth smiling back at him. "Aye," he agreed.

She moved forward and leaned on the rail next to him. "I like to come here to think. It seems to be the only place I can find peace."

Carson nodded and stared back out over the water. Jamie protested the lack of petting by squeezing Carson's arm again and hissing.

"He missed you," Elizabeth commented. She paused. "We all did."

"I don't deserve it," he said quietly, "Because of me the whole city was almost destroyed."

"You think that was your fault?" she asked in surprise.

"I gave them the means to attack you. I even attacked the Daedalus myself."

"And if you hadn't allowed them to escape and infected the Wraith with a deadly mutation we might all be dead right now," she emphasized.

He didn't answer, so she went on. "You took a big risk. It was very brave."

"I was a coward," he insisted. "I was willing to risk everything just for one person."

"And if you hadn't? We're all still here, Carson. And it's thanks to you."

The were both quiet for a few minutes.

"I killed them all," he whispered.

"What?"

"The Wraith. I killed them all. I didn't have to. I should have found another way."

"You did what you had to do," she told him seriously. "War is never easy or simple."

Carson sighed. "Next time, I'll find a better way."

"Let's hope there won't be a next time." Elizabeth turned to go and laid a comforting hand on his shoulder. "It's good to have you back, Carson."

He gave her a small smile. "Thank you, Elizabeth."

When she was gone, he looked out over the silver spires of Atlantis. _Yes_, he thought, _it was good to be back_.

FIN

_AN: Yay! This was my longest fic ever, and I hope you all enjoyed it! Thank you so much for your patience and reviews! Please leave a few last comments so I know what you think. Special thanks for my wonderful beta readers: Nalana, Geoff, and Nathan! Thank you once again for reading and I hope to write another story soon!_


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